Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.

The human centromere protein B (CENP-B), one of the centromere components, specifically binds a 17 bp sequence (the CENP-B box), which appears in every other alpha-satellite repeat. In the present study, the crystal structure of the complex of the DNA-binding region (129 residues) of CENP-B and the CENP-B box DNA has been determined at 2.5 A resolution. The DNA-binding region forms two helix-turn-helix domains, which are bound to adjacent major grooves of the DNA. The DNA is kinked at the two recognition helix contact sites, and the DNA region between the kinks is straight. Among the major groove protein-bound DNAs, this 'kink-straight-kink' bend contrasts with ordinary 'round bends' (gradual bending between two protein contact sites). The larger kink (43 degrees ) is induced by a novel mechanism, 'phosphate bridging by an arginine-rich helix': the recognition helix with an arginine cluster is inserted perpendicularly into the major groove and bridges the groove through direct interactions with the phosphate groups. The overall bending angle is 59 degrees, which may be important for the centromere-specific chromatin structure.

Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design.

As a first step in structure-based design of highly selective and potent Cdk4 inhibitors, we performed structure-based generation of a novel series of Cdk4 inhibitors. A Cdk4 homology model was constructed according to X-ray analysis of an activated form of Cdk2. Using this model, we applied a new de novo design strategy which combined the de novo design program LEGEND with our in-house structure selection supporting system SEEDS to generate new scaffold candidates. In this way, four classes of scaffold candidates including diarylurea were identified. By constructing diarylurea informer libraries based on the structural requirements of Cdk inhibitors in the ATP binding pocket of the Cdk4 model, we were able to identify a potent Cdk4 inhibitor N-(9-oxo-9H-fluoren-4-yl)-N'-pyridin-2-ylurea 15 (IC(50) = 0.10 microM), together with preliminary SAR. We performed a docking study between 15 and the Cdk4 model and selected a reasonable binding mode which is consistent with the SAR. Further modification based on the proposed binding mode provided a more potent compound, N-[(9bR)-5-oxo-2,3,5,9b-tetrahydro-1H-pyrrolo[2,1-a]isoindol-9-yl]-N'-pyridin-2-ylurea 26a (IC(50) = 0.042 microM), X-ray analysis of which was accomplished by the soaking method. The predicted binding mode of 15 in Cdk4 was validated by X-ray analysis of the Cdk2-26a complex.

A novel approach for the development of selective Cdk4 inhibitors: library design based on locations of Cdk4 specific amino acid residues.

Identification of a selective inhibitor for a particular protein kinase without inhibition of other kinases is critical for use as a biological tool or drug. However, this is very difficult because there are hundreds of homologous kinases and their kinase domains including the ATP binding pocket have a common folding pattern. To address this issue, we applied the following structure-based approach for designing selective Cdk4 inhibitors: (1) identification of specifically altered amino acid residues around the ATP binding pocket in Cdk4 by comparison of 390 representative kinases, (2) prediction of appropriate positions to introduce substituents in lead compounds based on the locations of the altered amino acid residues and the binding modes of lead compounds, and (3) library design to interact with the altered amino acid residues supported by de novo design programs. Accordingly, Asp99, Thr102, and Gln98 of Cdk4, which are located in the p16 binding region, were selected as first target residues for specific interactions with Cdk4. Subsequently, the 5-position of the pyrazole ring in the pyrazol-3-ylurea class of lead compound (2a) was predicted to be a suitable position to introduce substituents. We then designed a chemical library of pyrazol-3-ylurea substituted with alkylaminomethyl groups based on the output structures of de novo design programs. Thus we identified a highly selective and potent Cdk4 inhibitor, 15b, substituted with a 5-chloroindan-2-ylaminomethyl group. Compound 15b showed higher selectivity on Cdk4 over those on not only Cdk1/2 (780-fold/190-fold) but also many other kinases (>430-fold) that have been tested thus far. The structural basis for Cdk4 selective inhibition by 15b was analyzed by combining molecular modeling and the X-ray analysis of the Cdk4 mimic Cdk2-inhibitor complex. The results suggest that the hydrogen bond with the carboxyl group of Asp99 and hydrophobic van der Waals contact with the side chains of Thr102 and Gln98 are important. Compound 15b was found to cause cell cycle arrest of the Rb(+) cancer cell line in the G(1) phase, indicating that it is a good biological tool.

Two new steroidal derivatives from the fruit body of Chlorophyllum molybdites.

Two new steroid derivatives, (22E,24R)-3alpha-ureido-ergosta-4,6,8(14),22-tetraene (1) and (22E,24R)-5alpha,8alpha-epidioxyergosta-6,9,22-triene-3beta-ol 3-O-beta-D-glucopyranoside (2) were isolated from the fruit bodies of Chlorophyllum molybdites (Agaricaceae). The structures were established by spectroscopic and chemical methods. These compounds exhibited cytotoxicity against Kato III cells.

Crystallographic approach to identification of cyclin-dependent kinase 4 (CDK4)-specific inhibitors by using CDK4 mimic CDK2 protein.

Genetic alteration of one or more components of the p16(INK4A)-CDK4,6/cyclin D-retinoblastoma pathway is found in more than half of all human cancers. Therefore, CDK4 is an attractive target for the development of a novel anticancer agent. However, it is difficult to make CDK4-specific inhibitors that do not possess activity for other kinases, especially CDK2, because the CDK family has high structural homology. The three-dimensional structure of CDK2, particularly that bound with the inhibitor, has provided useful information for the synthesis of CDK2-specific inhibitors. The same approach used to make CDK4-specific inhibitors was hindered by the failure to obtain a crystal structure of CDK4. To overcome this problem, we synthesized a CDK4 mimic CDK2 protein in which the ATP binding pocket of CDK2 was replaced with that of CDK4. This CDK4 mimic CDK2 was crystallized both in the free and inhibitor-bound form. The structural information thus obtained was found to be useful for synthesis of a CDK4-specific inhibitor that does not have substantial CDK2 activity. Namely, the data suggest that CDK4 has additional space that will accommodate a large substituent such as the CDK4 selective inhibitor. Inhibitors designed to bind into this large cavity should be selective for CDK4 without having substantial CDK2 activity. This design principle was confirmed in the x-ray crystal structure of the CDK4 mimic CDK2 with a new CDK4 selective inhibitor bound.

Expression of heparanase in oral cancer cell lines and oral cancer tissues.

In the process of metastasis, cancer cells secrete several enzymes which degrade extracellular matrices (ECMs) and basement membranes (BMs) of blood vessels. One of them, heparanase, has been reported to be an important enzyme when metastatic cancer cells invade blood vessels. The enzyme cleaves heparan sulfate (HS), a main component of ECM and BM. In the present study, HS-degrading ability of several human oral cancer cell lines (HSC2, HSC3, HSC4, Ca9-22, NA, ACC3 and Ab-J) and tissues derived from human oral squamous cell carcinomas (both metastatic and non-metastatic) were investigated by measuring heparanase activities and levels of heparanase mRNA by a quantitative reverse transcriptase-polymerase chain reaction. The catalytic activities and the mRNA levels of heparanase showed a good agreement. Clinical demonstration of cancer metastasis generally correlated with high levels of heparanase activity and its mRNA. The results suggest that heparanase activity and its mRNA level are good diagnostic parameters for evaluating the metastatic properties of human oral cancer cells.

Design and synthesis of N-terminal cyclic motilin partial peptides: a novel pure motilin antagonist.

Motilin antagonist was designed and synthesized on the basis of the structure-activity relationship analysis of porcine motilin that we reported recently. The drug design was performed on a specific concept to reduce a flexibility of peptide conformation of porcine motilin partial peptide by its cyclization. The cyclic peptide was synthesized using Boc (tert-butyloxycarbonyl) solid phase methodology, followed by cyclization using the azide procedure, and tested for the binding activity to motilin receptor and smooth muscle contractile activity. The cyclic peptides 3, 4, and 5 showed antagonistic property on contraction assay (pA2 [the negative logarithm of molar concentration of antagonist causing a 2-hold shift to the right of the concentration-response curve for motilin]: 4.5, 4.34, and 4.04, respectively, in rabbit duodenum) and no contractile activity even at high concentration.

Structure-activity study of intact porcine motilin.

Biologically important sites on intact porcine motilin (pMTL) were explored using its partial peptides. The partial peptides were synthesized using Fmoc (9-fluorenylmethyloxycarbonyl) solid phase methodology, and tested for the binding activity to motilin receptor and the smooth muscle contractile activity. The results were as follows: important residues for the contractile activity were found to be Phe1, Ile4, and Tyr7, and an open space existed beyond the N-terminus between motilin and its receptor. On the model of interaction between motilin and motilin receptor evolved from these results, the three points of interaction, due to Phe1, Ile4, and Tyr7, and the presence of an open space were expected. The motilin agonist and antagonist, designed on this model, will help the inquiry into motilin associated diseases.

Insulin and glucagon secretion in goats (Capra hircus Linnaeus) exposed to cold.

Cold exposure significantly decreased the insulin response to the intravenous injection of arginine, butyrate and tolbutamide, and tended to reduce the response to glucose in goats. The glucagon responses to these test materials were not different between warm and cold environments. Intravenous phentolamine infusion tended to increase, and propranolol infusion decreased insulin secretion more effectively in the cold than in the warm environment. It is concluded that cold exposure decreases insulin secretion in response to a variety of stimuli in goats.

GM-109: a novel, selective motilin receptor antagonist in the smooth muscle of the rabbit small intestine.

The pharmacological properties of the cyclic peptide Phe-cyclo[Lys-Tyr(3-tBu)-beta Ala-].trifluoroacetate (GM-109), a selective motilin antagonist, were investigated in the smooth muscle of the rabbit small intestine. GM-109 (0.1-3 microM) competitively inhibited contractions induced by porcine motilin (pMTL) in rabbit isolated duodenum longitudinal strips, with a pA2 value of 7.37 +/- 0.24. However, the contractile response to acetylcholine, to substance P, to prostaglandin F2 alpha and to KCl was unaffected by 10 microM GM-109 in the same preparation. Both GM-109 and pMTL competitively inhibited 125I-pMTL binding to motilin receptors in a homogenate of the rabbit small intestinal smooth muscle tissue. The pKi value of GM-109 and the pKd value of unlabeled pMTL were 7.99 +/- 0.04 and 9.25 +/- 0.06 (each n = 5), respectively. These results indicate that GM-109 is a selective and competitive motilin receptor antagonist in the smooth muscle of the rabbit small intestine. Thus this compound may be a useful pharmacological tool for examining the functional role(s) of motilin.

Determination of amino acids in human plasma by liquid chromatography with postcolumn ninhydrin derivatization using a hydroxyapatite cartridge for precolumn deproteination.

Amino acids in human plasma were determined by liquid chromatography with postcolumn ninhydrin derivatization using a hydroxyapatite cartridge for precolumn deproteination. S-Carboxymethyl-L-cysteine, D-phenylglycine and S-aminoethyl-L-cysteine were found to be suitable internal standards. The proposed method is simple, rapid (deproteination time less than 1 min) and reproducible [relative standard deviation below 3% except for low-level aspartic acid (n = 3)]. The average recovery of 25 amino acids was above 90%. The elution time of amino acids in human plasma was approximately 2 h. Protein binding of tryptophan was also determined by the proposed method. The analytical data for amino acids in human plasma deproteinated using the proposed and published methods (5-sulphosalicylic acid and ethanol) were compared.

Renal handling of phosphate can predict height velocity during growth hormone therapy for short children.

Renal tubular reabsorption of phosphate in response to GH administration was studied in 28 short Japanese children, aged 5-11 yr (height SD score, less than -2.0 SD). Three groups included a classical GH deficiency (group 1; n = 12), a partial GH deficiency (group 2; n = 7), and children with non-GH deficiency (group 3; n = 9), depending on the peak response of serum GH in four provocative tests. Serum phosphorus, alkaline phosphatase, insulin-like growth factor-I (IGF-I), osteocalcin, and ratio of the maximum tubular reabsorption rate for phosphorus to the glomerular filtration rate (Tmp/GFR) were all significantly lower in group 1 compared with findings in groups 2 and 3 (P less than 0.05, P less than 0.01, and P less than 0.001). After the administration of GH (0.1 U/kg.day) for 4 consecutive days, increments in serum phosphorus and Tmp/GFR were significantly higher in group 1 than in group 2 (P less than 0.01 and P less than 0.01) or group 3 (P less than 0.01 and P less than 0.01), whereas the increment in IGF-I was similar in all 3 groups, and the levels of serum alkaline phosphatase and osteocalcin remained unchanged in all 3 groups. The calculated ratio of the increment in Tmp/GFR to the increment in IGF-I (delta Tmp/GFR/delta IGF-I) was highest in group 1, intermediate in group 2, and lowest in group 3 (P less than 0.001). One year after the GH treatment (0.5 U/kg.week), height velocity was 7.9 +/- 2.2 cm/yr in group 1 and 5.9 +/- 1.2 cm/yr in group 2; no child in group 3 was treated. When the above calculated parameters, delta Tmp/GFR/delta IGF-I and increment in height velocity (difference between pre- and posttherapy values), were taken into account, there was a significant positive correlation (n = 19; r = 0.78; P less than 0.001). This parameter can be used for purposes of predicting the outcome after 1 yr of GH therapy.

Interleukin 6 inhibits delayed-type hypersensitivity and the development of adjuvant arthritis.

We studied the effect of interleukin 6 (IL 6) on the delayed-type hypersensitivity (DTH). In mice immunized with sheep red blood cells (SRBC), a DTH response was evoked by antigen challenge into the hind paw 5 days after immunization. The magnitude of the response was assessed by footpad swelling measured 24 h after antigen challenge. IL 6 significantly suppressed the DTH in its induction phase in a dose-dependent manner when administered s.c. into the back at a dose of greater than 2.5 micrograms twice a day (5 micrograms/day) for 5 consecutive days from the day of immunization (day 0) to 1 day before antigen challenge (day 4). Heat-inactivated IL 6 did not suppress the DTH response. Furthermore, the suppressive activity of IL 6 was completely abolished by affinity chromatography on an anti-IL 6 antibody. This suppression was also obtained when IL 6 was administered only on day 0 and day 1, but not on days 3 and 4. This indicates that IL 6 acts on the early part of the induction phase of DTH development. Furthermore, footpad swelling was suppressed even by the administration of IL 6 after antigen challenge. These results show that IL 6 suppresses both the induction and effector phases of DTH. To confirm further this inhibitory effect of IL 6, we examined its effect on the development of adjuvant arthritis in rats. Administration of IL 6 also significantly suppressed the development of adjuvant arthritis.

UMC, another Cromer-related blood group antigen.

An antibody found in the serum of a Japanese blood donor detects a new high-frequency red cell antigen named UMC. UMC is absent from Inab phenotype cells, weakly expressed on Dr(a-) cells, and destroyed by alpha-chymotrypsin but not trypsin treatment of red cells. UMC is, therefore, a Cromer-related antigen. Immunoblotting with anti-UMC showed that UMC antigen, in common with other Cromer-related antigens, is carried on a red cell surface glycoprotein with an apparent molecular weight of 70,000, which presumably is the complement regulatory protein decay-accelerating factor.

Effect of serum magnesium concentration on renal handling of phosphate in a patient with primary hypomagnesemia.

We examined a case of primary hypomagnesemia with associated hypocalcemia and hyperphosphatemia. It was found, on treatment with magnesium, that there was a significant negative correlation between the serum magnesium level and the percent tubular reabsorption of phosphate, especially when the serum magnesium concentration was above 1.0 mg/dl, in the patient. It is suggested that the serum magnesium concentration might play an important role in urinary phosphate excretion, probably in relation to the parathyroid hormone function.

Long-dormant invasive mole associated with multiple malignancies.

A 65-year-old previously healthy housewife, gravida 3, para 3, was first diagnosed as Stage Ib carcinoma of the uterine cervix (poorly differentiated squamous cell carcinoma) and admitted. The external radiation of 5400 rad by telecobalt source was performed. No intracavitary radiation was added. After about 7 1/2 years the patient noticed a tumor of fist size on her buttocks, but she did not present in our clinic regularly. Because of enlarging tumor and general malaise she was readmitted a year later. On the fifth hospital day she died with ileus. Autopsy revealed osteosarcoma of buttocks in the radiation field, stomach cancer (tubular adenocarcinoma) with perforated peritonitis, and invasive mole of the uterine corpus. The patient's last pregnancy terminated as a full-term delivery at 26 years of age and she was 43 years at her menopause. The dormant period of invasive mole was 47 years after her last pregnancy, 30 years after her menopause, and at least 8 years after pelvic radiation.