Unexpected Rearrangement Reactions of the 14-Aminonaltrexone Skeleton

The reaction of 14-aminonaltrexone with acetic anhydride was found to produce a range of different novel compounds between the free compound and its hydrochloride. The hydrochloride produced a compound with an acetylacetone moiety, whereas the free form produced a compound with a pyranopyridine moiety. Efforts to isolate reaction intermediates and density functional theory calculations have elucidated those formation mechanisms with both bearing the novel morphinan-type skeleton. Furthermore, a derivative with the acetylacetone moiety showed binding to opioid receptors.

Design and Synthesis of Orexin 1 Receptor-Selective Agonists

Orexins are a family of neuropeptides that regulate various physiological events, such as sleep/wakefulness as well as emotional and feeding behavior, and that act on two G-protein-coupled receptors, i.e., orexin 1 (OX₁R) and orexin 2 receptors (OX₂R). Since the discovery that dysfunction of the orexin/OX₂R system causes the sleep disorder narcolepsy, several OX₂R-selective and OX_1/2R dual agonists have been disclosed. However, an OX₁R-selective agonist has not yet been reported, despite the importance of the biological function of OX₁R. Herein, we report the discovery of a potent OX₁R-selective agonist, (R,E)-3-(4-methoxy-3-(N-(8-(2-(3-methoxyphenyl)-N-methylacetamido)-5,6,7,8-tetrahydronaphthalen-2-yl)sulfamoyl)phenyl)-N-(pyridin-4-yl)acrylamide [(R)-YNT-3708; EC₅₀ = 7.48 nM for OX₁R; OX₂R/OX₁R EC₅₀ ratio = 22.5]. The OX₁R-selective agonist (R)-YNT-3708 exhibited antinociceptive and reinforcing effects through the activation of OX₁R in mice.

Essential structure of orexin 1 receptor antagonist YNT-707: Conversion of the 16-cyclopropylmethyl group to the 16-sulfonamide group in D-nor-nalfurafine derivatives

The five-membered D-ring nalfurafine (D-nor-nalfurafine) derivatives with a 16-sulfonamide group were synthesized. Conversion of the 16-cyclopropylmethyl group to the 16-benzenesulfonamide group in the D-nor-nalfurafine derivatives drastically improved the orexin 1 receptor (OX₁R) antagonist activities. The intramolecular hydrogen bond between the 14-hydroxy and the 16-sulfonamide groups may play an important role in increasing the probability that the 6-amide group would be located at the lower side of the C-ring, leading to an active conformation for OX₁R. The assay results and the conformational analyses of the 14-OH, 14-H, and 14-dehydrated D-nor-nalfurafine derivatives suggested that the 14- and 16-substituents of the D-nor-nalfurafine derivatives had a greater effect on the affinities for the OX₁R than did the 14- and 17-substituents of nalfurafine derivatives.

Design and synthesis of novel orexin 2 receptor agonists based on naphthalene skeleton

A novel series of naphthalene derivatives were designed and synthesized based on the strategy focusing on the restriction of the flexible bond rotation of OX₂R selective agonist YNT-185 (1) and their agonist activities against orexin receptors were evaluated. The 1,7-naphthalene derivatives showed superior agonist activity than 2,7-naphthalene derivatives, suggesting that the bent form of 1 would be favorable for the agonist activity. The conformational analysis of 1,7-naphthalene derivatives indicated that the twisting of the amide unit out from the naphthalene plane is important for the enhancement of activity. The introduction of a methyl group on the 2-position of 1,7-naphthalene ring effectively increased the activity, which led to the discovery of the potent OX₂R agonist 28c (EC₅₀ = 9.21 nM for OX₂R, 148 nM for OX₁R). The structure-activity relationship results were well supported by a comparison of the docking simulation results of the most potent derivative 28c with an active state of agonist-bound OX₂R cryo-EM SPA structure. These results suggested important information for understanding the active conformation and orientation of pharmacophores in the orexin receptor agonists, which is expected as a chemotherapeutic agent for the treatment of narcolepsy.

Effect of removal of the 14-hydroxy group on the affinity of the 4,5-epoxymorphinan derivatives for orexin and opioid receptors

To investigate the contribution of hydrogen bonding between the 14-hydroxy group and the 6-amide chain on the binding affinity of nalfurafine toward KOR and OX₁R, we prepared the 14-H and 14-dehydrated nalfurafine and their five-membered D-ring nalfurafine (D-nor-nalfurafine) derivatives. The 14-H and 14-dehydrated nalfurafine derivatives showed almost the same affinity for KOR as nalfurafine and more potent affinity for OX₁R. On the other hand, 14-H and 14-dehydrated D-nor-nalfurafine derivatives showed weak affinity for KOR and almost no affinity for OX₁R. The conformational analyses suggested that the 6-amide chains of the nalfurafine derivatives are mainly oriented just at or downward from the C-ring, while those of the D-nor-nalfurafine derivatives were mainly oriented toward the upper side of the C-ring even in the absence of the 14-hydroxy group. We postulated that the ion-dipole interaction between the 6-amide and the 16-nitrogen might stabilize the upwardly oriented 6-amide group. These results suggested that the 14-hydroxy group and the ion-dipole interaction would play important roles in the orientation of the 6-amide group, which might control the affinity between KOR and OX₁R.

Discovery of attenuation effect of orexin 1 receptor to aversion of nalfurafine: Synthesis and evaluation of D-nor-nalfurafine derivatives and analyses of the three active conformations of nalfurafine

The D-nor-nalfurafine derivatives, which were synthesized by contraction of the six-membered D-ring in nalfurafine (1), had no affinity for orexin 1 receptors (OX₁Rs). The 17N-lone electron pair in 1 oriented toward the axial direction, while that of D-nor-derivatives was directed in the equatorial configuration. The axial lone electron pair can form a hydrogen bond with the 14-hydroxy group, which could push the 6-amide side chain toward the downward direction with respect to the C-ring. The resulting conformation would be an active conformation for binding with OX₁R. The dual affinities of 1 for OX₁R and κ opioid receptor (KOR) led us to elucidate the mechanism by which only 1 showed no aversion but U-50488H. Actually, 1 selectively induced severe aversion in OX₁R knockout mice, but not in wild-type mice. These results well support that OX₁R suppresses the aversion of 1. This is the elucidation of long period puzzle which 1 showed no aversion in KOR.

Discovery of Peripheral κ-Opioid Receptor Agonists as Novel Analgesics

κ-Opioid receptor agonists with high selectivity over the μ-opioid receptor and peripheral selectivity are attractive targets in the development of drugs for pain. We have previously attempted to create novel analgesics with peripheral selective κ-opioid receptor agonist on the basis of TRK-820. In this study, we elucidated the biological properties of 17-hydroxy-cyclopropylmethyl and 10α-hydroxy derivatives. These compounds were found to have better κ-opioid receptor selectivity and peripheral selectivity than TRK-820.

Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation

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Keap1 is useful target for the design of drugs that regulate the response to oxidative stresses.

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We determined two complex crystal structures of Keap1 with a small molecule ligand.

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The ligand binds to Keap1 so as to mimic the physiological substrate Nrf2.

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From molecular dynamics simulation results, the binding modes observed may be atypical in solution.

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Key residues for ligand binding are common between crystal and MD structures.

Keap1 protein acts as a cellular sensor for oxidative stresses and regulates the transcription level of antioxidant genes through the ubiquitination of a corresponding transcription factor, Nrf2. A small molecule capable of binding to the Nrf2 interaction site of Keap1 could be a useful medicine. Here, we report two crystal structures, referred to as the soaking and the cocrystallization forms, of the Kelch domain of Keap1 with a small molecule, Ligand1. In these two forms, the Ligand1 molecule occupied the binding site of Keap1 so as to mimic the ETGE motif of Nrf2, although the mode of binding differed in the two forms. Because the Ligand1 molecule mediated the crystal packing in both the forms, the influence of crystal packing on the ligand binding was examined using a molecular dynamics (MD) simulation in aqueous conditions. In the MD structures from the soaking form, the ligand remained bound to Keap1 for over 20 ns, whereas the ligand tended to dissociate in the cocrystallization form. The MD structures could be classified into a few clusters that were related to but distinct from the crystal structures, indicating that the binding modes observed in crystals might be atypical of those in solution. However, the dominant ligand recognition residues in the crystal structures were commonly used in the MD structures to anchor the ligand. Therefore, the present structural information together with the MD simulation will be a useful basis for pharmaceutical drug development.

Structural basis for platelet antiaggregation by angiotensin II type 1 receptor antagonist losartan (DuP-753) via glycoprotein VI

GPVI is a key receptor for collagen-induced platelet activation. Loss or inhibition of GPVI causes only mildly prolonged bleeding times but prevents arterial thrombus formation in animal models. Therefore, GPVI is considered to be a potent target molecule for therapy of thrombotic diseases. Recently, it was reported that the AT(1)-receptor antagonist losartan (DuP-753) and EXP3179 inhibit platelet adhesion and aggregation via GPVI. However, it is still not clear how losartan is associated with inhibition of binding between GPVI and collagen at the molecular level. Here, we show by NMR that losartan directly interacts with the hydrophobic region consisting of strands C' and E in the N-terminal Ig-like domain of GPVI. A reliable GPVI-losartan complex model is presented by using a combination of NMR data and in silico tools. These data indicated that the phenyl group with the tetrazole ring in losartan plays a crucial role in the interaction with GPVI.

Structural and interaction analysis of glycoprotein VI-binding peptide selected from a phage display library

Glycoprotein VI (GPVI) is a major collagen receptor on the platelet surface that recognizes the glycine-proline-hydroxyproline (GPO) sequence in the collagen molecule and plays a crucial role in thrombus formation. Inhibitors that block the interaction of GPVI with collagen have potential for use as antithrombotic drugs. For low molecular weight drug design for GPVI, it is essential to obtain precise structural and interaction information about GPVI-binding ligands. However, experimentally obtained structural and interaction information of small ligands, such as peptides, in the GPVI-bound state has not been reported. In this study, by screening a phage-displayed peptide library, we discovered a novel peptide ligand (pep-10L; YSDTDWLYFSTS) without any similarities to the sequence of collagen that inhibits GPVI-GPO binding. Systematic Ala scanning in surface plasmon resonance experiments and a saturation transfer difference NMR experiment revealed that Trp(6), Leu(7), Phe(9), and Ser(10) residues in the pep-10L peptide interacted with GPVI. Furthermore, the GPVI-bound conformation of the pep-10L peptide was determined using transferred nuclear Overhauser effect analysis. The obtained structure has revealed that the central part of pep-10L (Asp(5)-Phe(9)) has a helical conformation, the side chains of Trp(6), Leu(7), and Phe(9) form a hydrophobic side in the helix, and the Tyr(8) side chain faces the opposite direction from the hydrophobic side. Computational docking prediction has shown that the hydrophobic side of pep-10L sticks in the hydrophobic groove on the GPVI surface, which corresponds to the putative collagen-related peptide binding groove. These data could enable the structure-guided development of a small molecule GPVI antagonist.

Beta(1)-selective agonist (-)-1-(3,4-dimethoxyphenetylamino)-3-(3,4-dihydroxy)-2-propanol [(-)-RO363] differentially interacts with key amino acids responsible for beta(1)-selective binding in resting and active states

(-)-1-(3,4-Dimethoxyphenetylamino)-3-(3,4-dihydroxy)-2-propanol [(-)-RO363] is a highly selective beta(1)-adrenergic receptor (beta(1)AR) agonist. To study the binding site of beta(1)-selective agonist, chimeric beta(1)/beta(2)ARs and Ala-substituted beta(1)ARs were constructed. Several key residues of beta(1)AR [Leu(110) and Thr(117) in transmembrane domain (TMD) 2], and Phe(359) in TMD 7] were found to be responsible for beta(1)-selective binding of (-)-RO363, as determined by competitive binding. Based on these results, we built a three-dimensional model of the binding domain for (-)-RO363. The model indicated that TMD 2 and TMD 7 of beta(1)AR form a binding pocket; the methoxyphenyl group of N-substituent of (-)-RO363 seems to locate within the cavity surrounded by Leu(110), Thr(117), and Phe(359). The amino acids Leu(110) and Phe(359) interact with the phenyl ring of (-)-RO363, whereas Thr(117) forms hydrogen bond with the methoxy group of (-)-RO363. To examine the interaction of these residues with beta(1)AR in an active state, each of the amino acids was changed to Ala in a constitutively active (CA)-beta(1)AR mutant. The degree of decrease in the affinity of CA-beta(1)AR for (-)-RO363 was essentially the same as that of wild-type beta(1)AR when mutated at Leu(110) and Thr(117). However, the affinity was decreased in Ala-substituted mutant of Phe(359) compared with that of wild-type beta(1)AR. These results indicated that Leu(110) and Thr(117) are necessary for the initial binding of (-)-RO363 with beta(1)-selectivity, and interaction of Phe(359) with the N-substituent of (-)-RO363 in an active state is stronger than in the resting state.

[Knowledge used in duration judgments of two moving objects]

Forty-nine undergraduates observed two cars traveling in the same direction on a CRT display for various duration. They then chose the car that they believed had run longer, and gave the reason for their choice. There were three types of tasks. Correct judgment was possible for the first type, by logically applying either of two pieces of knowledge about duration: "duration equals temporal end point minus temporal start point" (Knowledge alpha) or "duration equals distance divided by speed" (Knowledge beta). Knowledge alpha alone was useful for the second type, while only Knowledge beta led to correct judgment for the third. Main results were as follows: (1) Undergraduates were more likely to use Knowledge alpha than beta regardless of the types. (2) None of repeatedly making judgment, thinking about reasons for judgment, or receiving failure feedback was very helpful making participants become aware of necessity of using Knowledge beta for the third type. (3) Only some 20% of undergraduates were able to use proper knowledge specifically required for each type.

Binding pockets of the beta(1)- and beta(2)-adrenergic receptors for subtype-selective agonists

We examined the subtype-selective binding site of the beta-adrenergic receptors (betaARs). The beta(1)/beta(2)-chimeric receptors showed the importance of the second and seventh transmembrane domains (TM2 and TM7) of the beta(2)AR for the binding of the beta(2)-selective agonists such as formoterol and procaterol. Alanine-substituted mutants of TM7 of the beta(2)AR showed that Tyr(308,) located at the top of TM7, mainly contributed to beta(2) selectivity. However, Tyr(308) interacted with formoterol and procaterol in two different ways. The results of Ala- and Phe-substituted mutants indicated that the phenyl group of Tyr(308) interacted with the phenyl group in the N-substituent of formoterol (hydrophobic interaction), and the hydroxyl group of Tyr(308) interacted with the protonated amine of procaterol (hydrophilic interaction). In contrast to beta(2)AR, TM2 is a major determinant that beta(1)-selective agonists such as denopamine and T-0509 bound the beta(1)AR with high affinity. Three amino acids (Leu(110), Thr(117), and Val(120)) in TM2 of the beta(1)AR were identified as major determinants for beta(1)-selective binding of these agonists. Three-dimensional models built on the basis of the predicted structure of rhodopsin showed that Tyr(308) of the beta(2)AR covered the binding pocket formed by TM2 and TM7 from the upper side, and Thr(117) of the beta(1)AR located in the middle of the binding pocket to provide a hydrogen bonding for the beta(1)-selective agonists. These data indicate that TM2 and TM7 of the betaAR formed the binding pocket that binds the betaAR subtype-selective agonists with high affinity.

Contribution of stimulus attributes to errors in duration and distance judgments--a developmental study

In Matsuda's 1996 study, 4- to 11-yr.-old children (N = 133) watched two cars running on two parallel tracks on a CRT display and judged whether their durations and distances were equal and, if not, which was larger. In the present paper, the relative contributions of the four critical stimulus attributes (whether temporal starting points, temporal stopping points, spatial starting points, and spatial stopping points were the same or different between two cars) to the production of errors were quantitatively estimated based on the data for rates of errors obtained by Matsuda. The present analyses made it possible not only to understand numerically the findings about qualitative characteristics of the critical attributes described by Matsuda, but also to add more detailed findings about them.

Evolving catalytic antibodies in a phage-displayed combinatorial library

In vitro affinity maturation for evolving catalytic antibodies has been demonstrated by generating a diverse repertoire of the appropriate complementarity-determining regions on a phage surface. Phage display is followed by a selection based on binding to an altered antigen that was not used at the time of immunization, and provides variants with new catalytic activity and substrate specificity. This library format reduces the time needed to isolate the desired catalytic antibody fragments to under 2 weeks.

Solution structure of ferredoxin from the thermophilic cyanobacterium Synechococcus elongatus and its thermostability

The three-dimensional structure of ferredoxin, purified from the thermophilic cyanobacterium Synechococcus elongatus, was determined in aqueous solution by two-dimensional proton nuclear magnetic resonance. In addition to the 946 distance constraints from nuclear Overhauser effect connectivities, we added 241 distance constraints derived from the crystal structure of Spirulina platensis ferredoxin to the 19 residues close to the [2Fe-2S] iron-sulfur center, where crosspeaks disappeared due to paramagnetic effects. The atomic root-mean-square difference of the ten converged structures from the mean structure was 0.61(+/-0.12) A for backbone atoms (N, C(alpha), C'). The main-chain structure was almost the same as the crystal structures of other mesophile ferredoxins, but comparison of the side-chain structures revealed an extension of the hydrophobic core, a unique hydrophobic patch on the surface of the large beta-sheet, and two unique charge networks in this thermostable ferredoxin structure, some of which might contribute to thermostability.

Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization

Specific molecular interactions involved in catalysis by antibody 6D9 were investigated by site-directed mutagenesis. The catalytic antibody 6D9, which was generated against a transition state analog (III), hydrolyzes a non-bioactive chloramphenicol monoester derivative (I) to produce chloramphenicol (II). Construction of a three-dimensional molecular model of 6D9 and sequence comparison within a panel of related antibodies suggested candidates for catalytic residues, His (L27d), Tyr (L32), Tyr (H58) and Arg (H100b); these were targeted for the site-directed mutagenesis study. The Y-H58-F and R-H100b-A mutants possessed catalytic activities comparable to that of the wild-type, and the Y-H58-H and Y-L32-F mutant displayed an approximately fivefold decrease in k(cat)/Km. In the transition state analysis, the plots of logK(TSA) versus log(k(cat)/Km) for the mutants are linear, with a slope of approximately 1.0, indicating that the entire hapten-binding energy in the mutants is also utilized to bind the transition state and to accelerate the catalysis. In addition, a dramatic change in the catalytic activity was observed when the histidine residue (27d) in the CDR1 light chain was replaced with alanine. The H-L27d-A mutant had no detectable catalytic activity. This mutation led to a large, 40-fold reduction in transition state binding, with no change in substrate binding. Coupled with the previous kinetic studies and chemical modifications of the intact 6D9 antibody, this mutagenesis study has demonstrated that His L27d plays an essential role in stabilization of the transition state, the mechanism of catalysis by the 6D9 antibody.

Interaction between the amino-terminal SH3 domain of CRK and its natural target proteins

CRK is a human homolog of chichen v-Crk, which is an adaptor protein. The SH2 domain of CRK binds to several tyrosine-phosphorylated proteins, including the epidermal growth factor receptor, p130(Cas), Shc, and paxillin. The SH3 domain, in turn, binds to cytosolic proteins of 135-145, 160, 180, and 220 kDa. We screened expression libraries by Far Western blotting, using CRK SH3 as a probe, and identified partial cDNA sequences of four distinct proteins, including C3G, DOCK180, EPS15, and clone ST12. The consensus sequence of the CRK SH3 binding sites as deduced from their amino acid sequences was Pro+3-Pro+2-X+1-Leu0-Pro-1-X-2-Lys-3. The interaction of the CRK SH3 domain with the DOCK180 peptide was examined with an optical biosensor, based on the principles of surface plasmon resonance. A low dissociation constant of the order of 10(-7) resulted from a high association rate constant (kassoc = 3 x 10(4)) and low dissociation rate constant (kdiss = 3 x 10(-3)). All CRK-binding proteins except clone ST12 also bound to another adaptor protein, Grb2. Mutational analysis revealed that glycine at position +1 of ST12 inhibited the binding to Grb2 while retaining the high affinity binding to CRK SH3. The result suggests that the amino acid at position +1 also contributes to the high affinity binding of the peptides to the SH3 domain of Grb2, but not to that of CRK.

Developmental characteristics of topographic EEG in school-age children using an autoregressive model

Developmental characteristics of the resting EEG were investigated in 47 school-age children using statistical analysis. Total and component EEG power were statistically analyzed between the subject groups from 7 to 14 year-old using our autoregressive pattern discrimination system. In early school-age children, significant topographic differences were seen in theta waves, while in late school-age children, the differences were found in alpha waves in the frontal and occipital regions, and in beta waves in the frontal region.

Determinants of protein side-chain packing

The problem of protein side-chain packing for a given backbone trace is investigated using 3 different prediction models. The first requires an exhaustive search of all possible combinations of side-chain conformers, using the dead-end elimination theorem. The second considers only side-chain-backbone interactions, whereas the third neglects side-chain-backbone interactions and instead keeps side-chain-side-chain interactions. Predictions of side-chain conformations for 11 proteins using all 3 models show that removal of side-chain-side-chain interactions does not cause a large decrease in the prediction accuracy, whereas the model having only side-chain-side-chain interactions still retains a significant level of accuracy. These results suggest that the 2 classes of interactions, side-chain-backbone and side-chain-side-chain, are consistent with each other and work concurrently to stabilize the native conformations. This is confirmed by analyses of energy spectra of the side-chain conformations derived from the fourth prediction model, the Independent model, which gives almost the same quality of the prediction as the dead-end elimination. The analyses indicate that the 2 classes of interactions simultaneously increase the energy difference between the native and nonnative conformations.

A common ancestry for multiple catalytic antibodies generated against a single transition-state analog

Immunization with a single haptenic transition-state analog generates a few catalytic antibodies among the dozens of antibodies capable of binding the hapten. The diversity of the immune response has raised some fundamental issues, such as How do catalytic and noncatalytic antibodies differ on a structural basis? To address this issue, the variable region primary sequences of 11 antibodies (including 6 catalytic and 5 noncatalytic antibodies) elicited against a single haptenic transition-state analog were deduced from cDNA sequences. Cluster analyses using phylogenetic trees constructed by the neighbor-joining method have revealed that the amino acid sequences of noncatalytic antibodies bear no relationship to one another, while the catalytic antibodies share significant structural identity. Furthermore, no catalytic antibodies possessing amino acid sequences with high homology to those of noncatalytic antibodies were detected. Five catalytic antibodies examined showed 89-95% and 74-84% sequence homologies in the complete light- and heavy-chain variable regions, respectively. Thus, it seems likely that the catalytic antibodies elicited against a single hapten use the canonical set of variable region genes. Interestingly, one catalytic antibody showed only limited sequence similarity to the other catalytic antibodies and was found to exhibit a distinctly different substrate specificity. From the broad range of their binding constants to the hapten, it is unlikely that highly homologous catalytic antibodies are generated as a result of simple high-affinity choices. These results emphasize the utility of rationally designed transition-state analogs for the induction of antibody molecules with catalytic activity.

Extrarenal Wilms' tumour

Extrarenal Wilms' tumour is rare and its imaging has received scant mention in the literature. We describe a 2-year-old boy with a firm mass in the right flank. CT, MRI and ultrasonography showed an inhomogeneous solid mass located in the retroperitoneum, which was separate from the right kidney. Angiography showed an enlarged right gonadal artery and irregularly tortuous vessels in the tumour similar to intrarenal Wilms' tumour ("spider leg" or "creeping vine" appearance). Histopathological examination confirmed an extrarenal Wilms' tumour.