Molecular structures of two indole alkaloids, evodiamine and rutecarpine, from evodia fruit

Evodiamine,C19H17N3, is orthorhombic, P21212, a=13.654(2) Å, b=20.727(1) Å, c=5.2370(3) Å, V=1482.1(2) Å 3, Z=4. Rutecarpine, C18H13N3O, is monoclinic, P21/a, a= 26.909(1) Å, b=7.398(1) Å, c=14.468(1) Å, ß=98.672(5)°, V=2847.3(4) Å 3, Z=8. Although rutecarpine takes an essentially planar structure, evodiamine is folded in the middle of the molecule and the two halves are nearly perpendicular to each other. The marked differences of the three-dimensional structures is considered to be responsible for the significant difference of the body temperature retaining effects of these alkaloids.

All-trans-retinoic acid inhibits tumour growth of malignant pleural mesothelioma in mice

Malignant pleural mesothelioma (MPM) is an aggressive malignant tumour of mesothelial origin associated with asbestos exposure. Because MPM has limited response to conventional chemotherapy and radiotherapy, the prognosis is very poor. Several researchers have reported that cytokines such as interleukin (IL)-6 play an important role in the growth of MPM. Previously, it was reported that all-trans-retinoic acid (ATRA) inhibited the production and function of IL-6 and transforming growth factor (TGF)-beta1 in experiments using lung fibroblasts. We investigated whether ATRA had an inhibitory effect on the cell growth of MPM, the origin of which was mesenchymal cells similar to lung fibroblasts, using a subcutaneous xenograft mouse model. We estimated the tumour growth and performed quantitative measurements of IL-6, TGF-beta1 and platelet-derived growth factor (PDGF) receptor (PDGFR)-beta mRNA levels both of cultured MPM cells and cells grown in mice with or without the administration of ATRA. ATRA significantly inhibited MPM tumour growth. In vitro studies disclosed that the administration of ATRA reduced 1) mRNA levels of TGF-beta1, TGF-beta1 receptors and PDGFR-beta, and 2) TGF-beta1-dependent proliferation and PDGF-BB-dependent migration of MPM cells. These data may provide a rationale to explore the clinical use of ATRA for the treatment of MPM.

Inhibition of Plasminogen Activator Inhibitor-1

Objective— Serine protease inhibitors (serpin) play a central role in various pathological processes including coagulation, fibrinolysis, malignancy, and inflammation. Inhibition of serpins may prove therapeutic. As yet, however, only very few small molecule serpin inhibitors have been reported. For the first time, we apply a new approach of virtual screening to discover novel, orally active, small molecule serpin inhibitors and report their effectiveness.

Methods and Results— We focused on a clinically important serpin, plasminogen activator inhibitor-1 (PAI-1), whose crystal structure has been described. We identify novel, orally active molecules able to enter into the strand 4 position (s4A) of the A β-sheet of PAI-I as a mock compound. In vitro they specifically inhibit the PAI-1 activity and enhance fibrinolysis activity. In vivo the most effective molecule (TM5007) inhibits coagulation in 2 models: a rat arteriovenous (AV) shunt model and a mouse model of ferric chloride–induced testicular artery thrombosis. It also prevents the fibrotic process initiated by bleomycin in mouse lung.

Conclusions— The present study demonstrates beneficial in vitro and in vivo effects of novel PAI-1 inhibitors. Our methodology proves to be a useful tool to obtain effective inhibitors of serpin activity.

A novel class of prolyl hydroxylase inhibitors induces angiogenesis and exerts organ protection against ischemia

OBJECTIVE

Hypoxia inducible factor (HIF) plays a pivotal role in the adaptation to ischemic conditions. Its activity is modulated by an oxygen-dependent hydroxylation of proline residues by prolyl hydroxylases (PHD).

METHODS AND RESULTS

We discovered 2 unique compounds (TM6008 and TM6089), which inhibited PHD and stabilized HIF activity in vitro. Our docking simulation studies based on the 3-dimensional structure of human PHD2 disclosed that they preferentially bind to the active site of PHD. Whereas PHD inhibitors previously reported inhibit PHD activity via iron chelation, TM6089 does not share an iron chelating motif and is devoid of iron chelating activity. In vitro Matrigel assays and in vivo sponge assays demonstrated enhancement of angiogenesis by local administration of TM6008 and TM6089. Their oral administration stimulated HIF activity in various organs of transgenic rats expressing a hypoxia-responsive reporter vector. No acute toxicity was observed up to 2 weeks after a single oral dose of 2000 mg/kg for TM6008. Oral administration of TM6008 protected neurons in a model of cerebrovascular disease. The protection was associated with amelioration of apoptosis but independent of enhanced angiogenesis.

CONCLUSIONS

The present study uncovered beneficial effects of novel PHD inhibitors preferentially binding to the active site of PHD.

Use of amino acid composition to predict ligand-binding sites

A novel method for predicting the binding sites for druglike compounds on the surface of proteins was developed on the basis of the specific amino acid composition observed at the ligand-binding sites of ligand-protein complexes determined by X-ray analysis. A profile representing the preference of each of the 20 standard amino acids at the binding sites of druglike molecules was obtained for a small set of high-quality complex structures. An index termed propensity for ligand binding (PLB) was created from these profiles. The PLB index was used to predict the propensity of binding for 804 ligands at all potential binding sites on the proteins whose structures were determined by X-ray analysis. If the sites with the first two highest PLB indices are taken into consideration, the successfully predicted sites reached a high percentage of 86. The PLB prediction is relatively simple, but the validation study showed that it is both fast and accurate to detect ligand-binding sites, especially the binding sites of druglike molecules. Therefore, the PLB index can be used to predict the ligand-binding sites of uncharacterized protein structures and also to identify novel drug-binding sites of known drug targets.

[Docking method for drug discovery]

The effective integration of detailed structural information with computational chemistry, medicinal chemistry, and informatics transforms the dream of virtual screening into reality. One of the most important technologies essential for virtual screening is an effective docking method to find molecules that efficaciously interact with their target molecules. Since an efficient docking method can be a powerful tool for virtual screening, many different approaches to solving docking problems have been proposed. Docking problems have not yet been solved and none of the currently available programs are perfect in predicting all possible scenarios. Despite the limits and imperfections of the methodology, currently available docking methods are very useful for drug discovery. The basic principles and limits of docking methods together with matters for attention in applying the methods are described in this paper.

A Simple Method to Improve the Odds in Finding 'Lead-Like' Compounds from Chemical Libraries

A simple method of virtual screening is proposed. This method uses only chemical characters calculated from two dimensional chemical structures. Local and global chemical characters are represented by molecular fingerprint and trait, respectively. The trait is a newly introduced concept in this paper and it is expressed by a set of two dimensional (2D) molecular descriptors. In this study, both the molecular fingerprint and the trait were used to represent drug-likeness of a group of molecules with a particular pharmacological activity. To learn about the molecular fingerprint and trait specific to a particular group of drugs, we used a database of drugs that are clinically used in Japan now. The molecular fingerprint and trait trained on these real drugs were used to predict drug-likeness of molecules in other chemical databases. In these chemical databases, an appreciable number of compounds that show the relevant pharmacological activity are contained. Some of these compounds are drugs clinically used abroad, but not in Japan. The prediction rate was judged by an enrichment factor. Despite the simplicity of the methodology, practical results were obtained. In the case of beta-adrenergic blockers, the enrichment factor of 66 was attained and nearly 57% of active molecules in the chemical databases were successfully covered.

Construction of an additional metal-binding site in human metallothionein-2

We have constructed a new metal-binding site in the human metallothionein-2 (hMT-2), using the protein as a scaffold to investigate the structure and function of metal-binding. Potential metal-binding sites were designed within hMT-2 on the basis of structures generated by homology modeling. Amino acid residues D11, C13, C26 and S28 in the beta-domain of hMT-2 (hMT-2beta) were found, by computer search, to form a potential tetrahedral Cys4 metal-binding site. Six mutant proteins were constructed with the following amino acid substitutions: D11C, S28C and D11C/S28C in hMT-2 and the same mutations in hMT-2beta, respectively. These single-mutant and double-mutant proteins bound one gram atom of cadmium or zinc ions per gram molecule of protein more than the corresponding wild-type proteins. The circular dichroism spectra suggested that the structures of the single-mutant proteins that bound Cd or Zn were similar to that of the D11C/S28C double-mutant proteins. To evaluate the metal-binding affinity of the mutant proteins, we performed pH titrations of wild-type and mutant proteins. The stability with changes in pH of all the mutant proteins was higher than that of the wild-type proteins, and that of the double-mutant D11C/S28C protein was highest. Consequently, it appears that we were able to create novel proteins that bound metal ions at high density and with high affinity.

G-CSF receptor-binding cyclic peptides designed with artificial amino-acid linkers

Designing small molecules that mimic the receptor-binding local surface structure of large proteins such as cytokines or growth factors is fascinating and challenging. In this study, we designed cyclic peptides that reproduce the receptor-binding loop structures of G-CSF. We found it is important to select a suitable linker to join two or more discontinuous sequences and both termini of the peptide corresponding to the receptor-binding loop. Structural simulations based on the crystallographic structure of KW-2228, a stable and potent analog of human G-CSF, led us to choose 4-aminobenzoic acid (Abz) as a part of the linker. A combination of 4-Abz with beta-alanine or glycine, and disulfide bridges between cysteins or homocysteins, gave a structure suitable for receptor binding. In this structure, the side-chains of several amino acids important for the interactions with the receptor are protruding from one side of the peptide ring. This artificial peptide showed G-CSF antagonistic activity in a cell proliferation assay.

Regimen of Tacrolimus-Based Immunosuppression With Basiliximab, Mycophenolate Mofetil, and Low-Dose Steroid Reduces Acute Rejection in Kidney Transplants

BACKGROUND

Acute rejection is a major problem in kidney transplantation. To reduce its likelihood, we investigated the efficacy and safety of an immunosuppressive regimen including tacrolimus, basiliximab, mycophenolate mofetil, and low-dose steroids.

METHODS

Fifty-seven patients, including 14 pediatric patients, were enrolled in this study. The mean age at the time of transplantation was 33.5 years, and the mean observation period was 8.2 months. The mean trough concentrations of FK at 1, 6, and 12 months posttransplant were 10.2, 6.6, and 6.0 ng/mL, respectively.

RESULTS

All recipients survived without graft loss. The cumulative incidence of acute rejection in adults was 2.3% and 8.4% at 6 and 12 months posttransplant, respectively. Of the adverse events, 11 recipients (19.3%) were positive for CMV antigenemia or had CMV infections. Four recipients (7.0%) exhibited mild hyperglycemia.

CONCLUSIONS

Our immunosuppressive regimen demonstrated favorable results, reducing the incidence of acute rejection without causing severe adverse events, especially in adults.

Reversibility from delayed hyperacute rejection in ABO-incompatible renal transplantation: histopathological findings of renal allograft biopsy

ABO-incompatible renal transplantation (ABOIRTx) tend to lead to blood type antibody-mediated rejection, the so-called delayed hyperacute rejection (DHAR), which results in short-term graft loss. To clarify the accurate incidence and prognostic value of DHAR among ABOIRTx, we reviewed biopsy specimens obtained from ABOKTx allografts with abrupt dysfunction during the early period after transplantation. Among 74 ABOIRTx patients, 34 patients displayed allograft dysfunction within 14 days following transplantation. The biopsy specimens were classified based on the Banff schema. The pathological diagnosis of ABO blood type antibody-mediated humoral rejection (ABO-AMHR) was made by the following 3 findings: Specimens with all of above-mentioned findings were categorized as severe ABO-AMHR; those with at least one findings, were categorized as mild ABO-AMHR. All patients were treated with steroid pulse therapy and/or modification of other immunosuppressants. Group 1 consisted of severe ABO-AMHR (n = 6); group 2 consisted of mild ABO-AMHR (n = 5); group 3 consisted of acute cellular rejection (n = 3); group 4 consisted of recovery phase of ATN (n = 11); group 5 consisted of calcineurin inhibitor toxicity (n = 2); and group 6 consisted of normal histology (n = 5). One of 6 patients (16%) in group 1 lost the graft because of DHAR irreversible by antirejection and anticoagulation therapy. However, there has been no clear definition of histpathological criteria for DHAR after ABO-incompatible kidney transplantation. The definition must prognosticate whether the rejection process is reversible.