Essential biomolecular functions often involve electron-related events such as chemical reactions and photoluminescence phenomena. Theoretical description of such electronic processes requires the use of quantum mechanics (QM), but the number of atoms that can be handled with QM is usually smaller than the number of atoms present in a single protein. A reasonable strategy is therefore to give priority to a few tens or hundreds of atoms in the system and deal with them quantum mechanically. Lower-priority atoms influence the event occurring in the higher-priority area; therefore, their effect should also be taken into account. Under these circumstances, a reasonable approach is to apply two or more different theoretical methods to differently prioritized subsystems. QM can be combined, for example, with less accurate yet much less demanding molecular mechanics (MM). Our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method allows for such hybrid calculations, and our group has been applying it to a wide range of biology-related problems. In this paper, we briefly explain the theoretical background and the procedure for the theoretical investigation of biological systems. Subsequently, we provide an overview of some of our recent studies of metalloenzymes and photobiology-related problems.
Due to the increase in computer power and the development of computational methods, it becomes possible to perform quantum mechanical calculations of very large molecules such as proteins that were previously exclusively treated with classical force field methods. We have developed the fragment molecular orbital (FMO) method aimed at biomolecular applications. One of the important applications of the method is in structure-based drug design because it provides accurate descriptions of various non-bonded interactions between a protein and its ligand. In this article, the FMO method will be described as well as its applications to the analysis of protein-ligand binding.
Reversible phosphorylation of proteins is a post-translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes, in particular the nature of transition state (TS), remains a subject of active debate. Structural evidence supports an associative TS, whereas physical organic studies point to a dissociative character. In this article, we briefly introduce our recent effort using the hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to resolve the controversy. We perform QM/MM simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP), which belongs to one of the largest phosphotransferase families characterized to data. Both phosphorylation and dephosphorylation reactions are investigated based on the two-dimensional energy surfaces along phosphoryl and proton transfer coordinates. The resultant structures of the active site at TS in both reactions have compact geometries but a less electron density of the phosphoryl group. This suggests that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database searches on phosphotransferases suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer.
It has been well established that disruption of JAK2 signaling regulation is involved in various hematopoietic disorders; however, the detailed mechanism by which abnormal activation of JAK2 exhibits transforming activity remains to be elucidated. The somatic JAK2 mutation (V617F) was identified in most patients with polycythemia vera (PV). Here, we show that JAK2 V617F mutant was constitutively active and exhibited tumorigenesis activity as a potent oncogene when erythropoietin receptor (EpoR) was co-expressed. To clarify the signaling pathway of JAK2 V617F mutant, we investigated the functional role of downstream transcription factor STAT5 in its induced cellular transformation and tumorigenesis in nude mice. Interestingly, JAK2 V617F mutant failed to exhibit transforming activity when STAT5 activation was inhibited utilizing EpoR mutant (HM). Furthermore, the expression of constitutively active STAT5 mutant (1*6) exhibited transforming activity. Taking these observations together, it is concluded STAT5 plays an essential role in EpoR-JAK2 V617F mutant-induced hematopoietic disorder and would be a good target for the treatment of PV.
The gene encoding lipin 1 was identified with a positional cloning approach that localized the causative mutation in fatty liver dystrophic (fld) mice, a mouse model of lipodystrophy. The fld mouse lacks normal adipose tissue in the body, and displays metabolic dysregulation such as obesity, insulin resistance, and hypertriglyceridemia. Lipin 1 is abundantly expressed in key metabolic tissues, including adipose tissue, skeletal muscle, and liver. In the cytosol, lipin 1 acts as an Mg2+-dependent phosphatidate phosphatase type-1 (PAP1), catalyzing a key step in the synthesis of glycerolipids. In the nucleus, lipin 1 acts as a transcriptional coactivator through its direct interaction with peroxisome proliferator-activated receptor (PPAR) γ coactivator-1α (PGC-1α) and PPARα. Through two distinct functions in the nucleus and cytosol, lipin 1 modulates lipid metabolism and glucose homeostasis. Here we will discuss recent developments in our understanding of the role of lipin 1 in lipid metabolism.
The mitogen-activated protein kinase (MAPK) pathways are signal transduction mechanisms that regulate many cellular processes in eukaryotic organisms, from yeasts to mammals. Multiple MAPKs regulate eukaryotic gene expression in response to various extracellular stimuli through phosphorylation of transcription factors. We have been studying the Pmk1 MAPK, a homologue of the mammalian ERK/MAPK in fission yeast. The Pmk1 MAPK regulates cell integrity and cell morphology. We have previously demonstrated that Atf1, a transcription factor downstream of the stress-activated MAPK pathway, serves also as a target of the Pmk1 MAPK signaling in fission yeast. Here, we identified ecm33+ gene, encoding a glycosyl-phosphatidylinositol (GPI)-anchored cell surface protein as a transcriptional target of Pmk1 and Atf1. The gene expression of ecm33+ is regulated by two transcription factors Atf1 and Mbx1. We also developed an in vivo real-time monitoring system of Atf1 or Mbx1 transcriptional activity, which enables to monitor the activation of the Pmk1 MAPK pathway by various stimuli. Finally, we demonstrated that Ecm33 is involved in the negative regulation of the Pmk1 MAPK signaling through the control of Ca2+ homeostasis. The ecm33 deleted cells displayed Ca2+ sensitivity and increased phosphorylation levels of Pmk1 MAPK. In addition, the Ecm33 overproducing cells displayed phenotypes closely similar to those of the pmk1 knockout cell. Collectively, Ecm33 plays a role in the negative feedback regulation of Pmk1 cell integrity signaling.
Progression of ischemic retinal diseases, such as diabetic retinopathy, is closely associated with pathological retinal angiogenesis mainly induced by vascular endothelial growth factor (VEGF). Anti-angiogenic therapy using anti-VEGF antibodies is effective in treating diabetic retinopathy, even though its efficacy is not long-lasting. Since many factors are involved in angiogenesis, it is reasonable to seek new therapeutic target molecules in pathological retinal angiogenesis. We have found that apelin/APJ system is involved in not only physiological but also pathological retinal angiogenesis using a mouse model of oxygen-induced retinopathy (OIR). Oxygen-induced vessel loss in the retinas of OIR model leads to a significant increase in the capillary density accompanied by abnormal vessel growth, similar to aneurysms, which are hardly detected in the retinas of control mice. Compared with age-matched control mice, retinal apelin expression was dramatically increased during retinal angiogenesis in OIR model. Immunostaining for APJ, apelin receptor, in retinal from OIR model revealed that APJ was localized in proliferating endothelial cells in the retinal vascular plexus. Retinal angiogenesis in the OIR model was rarely observed in apelin deficient mice, although temporal expression pattern of VEGF was similar to that of wild-type OIR model. In addition, clinical study showed that vitreous concentrations of apelin were significantly higher in the proliferative diabetic retinopathy group than in the control group. Taken together, these findings clearly suggest that apelin/APJ system may be a crucial factor for pathological retinal angiogenesis. Inhibition of this system could offer new therapeutic opportunities against ischemic retinopathy.
Fluorescence-derivatization-HPLC methods are powerful tools for performing the analysis of bioactive compounds with high sensitivity and selectivity. In this paper, the author reviews the development of the following four types of novel fluorescence-derivatization-HPLC analytical systems: (1) simultaneous HPLC analysis of melatonin and its related compounds through post-column electrochemical demethylation and fluorescence derivatization, (2) HPLC analysis of 5-hydroxyindoles based on fluorescence derivatization by online pre-column photocatalytic oxidation with benzylamine, (3) reagent peak-free HPLC analysis for aliphatic amines and amino acids using F-trap pyrene as a fluorous tag-bound fluorescence derivatization reagent, and (4) reagent peak-free HPLC analysis for carboxylic acids using a fluorous scavenging-derivatization method. The authors have also successfully applied these systems to biological and pharmaceutical analyses.
We performed a meta-analysis to assess antihypertensive effect, lipid metabolism, insulin resistance index, and body weight changes in patients with borderline diabetes and diabetes treated with angiotensin II receptor blockers (ARB) and dihydropyridine calcium channel blockers (CCB). Literatures for analysis were searched in MEDLINE, the Cochrane Library, and Japana Centra Revuo Medicina. Reports on randomized controlled trials in which the therapeutic results in borderline and diabetic patients were compared between those treated with ARB and CCB were retrieved, and 16 reports met the objective of this study. The efficacy in the two drug treatment groups were divided into 8 outcomes and evaluated. The efficacy outcomes on handling continuous data were integrated using the weighted mean difference, in which the random-effects model was selected for the statistical model. The statistical heterogeneity of each outcome was also tested. The systolic and diastolic blood pressures were significantly reduced in the CCB compared to the ARB treatment group. No significant differences were noted between the two groups in the triglyceride or low-density lipoprotein cholesterol level or body weight changes. It was shown that the CCB was more effective than ARB for the improvement of systolic and diastolic blood pressures in patients with borderline diabetes and diabetes, while no significant differences were noted in the efficacy other than the antihypertensive effect between ARB and CCB treatment groups. This study would provide information in selecting antihypertensive agents for borderline and diabetic patients.
Constipation can be caused by adverse drug reactions as a result of many drugs and might be induced by sleep disorders; however, the relative risk of its occurrence with individual drugs and the influence of sleep conditions have not been clarified. To clarify the relationship between constipation and various drugs in consideration of sleep disorders, we investigated the self-reported bowel habits, use of laxatives, and the Athens Insomnia Scale (AIS, a self-administered psychometric instrument to measure insomnia) in 344 inpatients on admission. They were divided into a constipation group (self-reported bowel habits of “Constipation” or “Occasional constipation” and/or use of laxatives, n=161) and a non-constipation group (both “Normal” and the non-use of laxatives, n=183). A comparison of the backgrounds of the two patient groups revealed significant differences in age, gender, number of used drugs, AIS score, hypothyroidism, chronic obstructive pulmonary disease, use of diuretics, coronary vasodilators, thyroid hormones, non-steroidal anti-inflammatory drugs, proton pump inhibitors, antidepressants, anti-anxiety drugs, and hypnotics. Multiple logistic regression analysis using these fourteen factors as autonomous variables showed that age (odds ratio [OR], 1.03; 95% confidence interval [CI], 1.01-1.04; p=0.007), female gender (OR, 1.96; 95% CI, 1.21-3.18; p=0.006), the AIS score (OR, 1.10; 95% CI, 1.02-1.18; p=0.010), and the use of hypnotics (OR, 2.33; 95% CI, 1.30-4.16; p=0.004) were significantly related to constipation; therefore, as hypnotics appear more likely to cause constipation than other drugs, they should be used with caution.
The chelate forming reaction between 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(4-methylpyridyl)porphine (OBTMPyP) and various metal ions, which belong mainly to 4th period and 7th-12th groups in the periodic table, was examined by the observing the absorption spectra. Because one chemical spicy, H-OBTMPyP, which is one protonated compound at an N atom of pyroll ring among 4 pyroll rings, was observed at pH 9.0, this pH was used to measure the changes of absorption spectra with metal ions. From these changes of absorption spectra of OBTMPyP with metal ions, OBTMPyP were seen to react easily with Cu2+, Zn2+, Mn2+, or Co2+ ion without other additional reagent or heating within 1 min at over 25°C. On the other hand, OBTMPyP reacted little with Ni2+, and was not all with Fe3+ (or Fe2+ reduced by ascorbic acid from Fe3+) under the same conditions. 5,10,15,20-tetrakis(4-methylpyridyl)porphine (TMPyP) also did not reacted metal ions above these conditions. The λmax of each Soret band differed. The stability constants (Ka value) of Cu-, Zn-, Mn- and Co-OBTMPyP was calculated by the change in absorbance of each band, and was 2.6×105, 3.6×105, 2.7×105 and 2.9×105 (dm3/mol), respectively. It was revealed that OBTMPyP and metal ions reacted at molar ratio of 1:1, and octabromination of porphine rings improved the reactivity with these ions.
Hot flash (HF) is the most common phenomenon in climacteric symptoms which often develop concomitantly with a decrease in estrogen in postmenopausal women. The onset mechanism of the hot flash is complicated and remains unclear. To date, some animal models of postmenopausal HF have been devised, but they are not fully available because of the difficulty in producing them. It is thought that hyperactivity of the central α-adrenergic system with a decrease in estrogen participates in the onset of postmenopausal HF. Therefore, in the present study, we examined whether a HF model could be easily produced by administering yohimbine (YOH), a presynaptic α2-adrenoceptor antagonist which promotes norepinephrine release, to female rats. HF-like symptoms such as a rise in tail skin temperature and a fall in rectal temperature were shown in the rats who received YOH (3 mg/kg) subcutaneously seven days after the ovariectomy (OVX). Such symptoms following YOH administration were observed in sham rats as well, but were much more clearly noted in OVX rats. We next examined the effects of various drugs, which are clinically effective against postmenopausal HF, on HF-like symptoms in YOH-treated OVX rats: clonidine, a presynaptic α2-adrenoceptor agonist which inhibits norepinephrine release; β-estradiol as an estrogen; and Keishibukuryogan, a Kampo medicine. These drugs inhibited HF-like symptoms in YOH-treated OVX rats. These results suggest that the activity of the α-adrenergic system is enhanced with a decrease in estrogen in OVX rats whereby YOH causes HF-like symptoms more conspicuously than in sham rats. Therefore, it is thought that YOH-treated OVX rats will be a novel and simple model of postmenopausal HF.
Bevacizumab is a monoclonal antibody that targets vascular endothelial growth factor (VEGF) for treatment of metastatic colorectal cancer. Recently, much evidence has suggested that bevacizumab-induced hypertension might be predictive of the effect of bevacizumab. The aim of our study is to retrospectively assess the relationship between the onset of hypertension and the activity of bevacizumab in Japanese metastatic colorectal cancer patients. Between July 2007 and December 2010, 36 patients (median age 66 years; 36-81 years) with metastatic colorectal cancer were assigned to receive bevacizumab in combination with either mFOLFOX6 (5-FU, levofolinate and oxaliplatin) or FOLFIRI (5-FU, levofolinate and irinotecan) at the Tokushima University Hospital. A patient who had increase by >20 mmHg in diastolic blood pressure or had increase to >150/100 mmHg or received antihypertensive treatment was defined as hypertensive. The objective response rate (ORR), disease control rate (DCR) and progression-free survival (PFS) were compared between the hypertensive group (n=10) and non-hypertensive group (n=26). ORR and DCR were 60.0% and 100%, respectively, in the hypertensive group and ORR and DCR were 23.1% and 80.8%, respectively, in the non-hypertensive group. These differences were statistically significant (p<0.05). The median PFS tended to be longer in the hypertensive group (65.0 weeks) than in the non-hypertensive group (40.0 weeks). Our data suggested that bevacizumab-induced hypertension may be predictive of the effect of bevacizumab in Japanese metastatic colorectal cancer patients.