Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro, and X-ray Crystallography

In drug discovery research, the selection of promising binding sites and understanding the binding mode of compounds are crucial fundamental studies. The current understanding of the proteins-ligand binding model extends beyond the simple lock and key model to include the induced-fit model, which alters the conformation to match the shape of the ligand, and the pre-existing equilibrium model, selectively binding structures with high binding affinity from a diverse ensemble of proteins. Although methods for detecting target protein binding sites and virtual screening techniques using docking simulation are well-established, with numerous studies reported, they only consider a very limited number of structures in the diverse ensemble of proteins, as these methods are applied to a single structure. Molecular dynamics (MD) simulation is a method for predicting protein dynamics and can detect potential ensembles of protein binding sites and hidden sites unobservable in a single-point structure. In this study, to demonstrate the utility of virtual screening with protein dynamics, MD simulations were performed on Trypanosoma cruzi spermidine synthase to obtain an ensemble of dominant binding sites with a high probability of existence. The structure of the binding site obtained through MD simulation revealed pockets in addition to the active site that was present in the initial structure. Using the obtained binding site structures, virtual screening of 4.8 million compounds by docking simulation, in vitro assays, and X-ray analysis was conducted, successfully identifying two hit compounds.

Association between cognitive social capital and all-cause mortality in Great East Japan Earthquake survivors: a prospective cohort study

OBJECTIVES

Cognitive social capital (SC), such as attitude, trust, or norms, may help improve resilience among survivors, thus improving their health. However, the association between cognitive SC and the risk of all-cause mortality among survivors after the natural disaster has never been investigated. The purpose of the present study is to investigate the association between cognitive SC and the risk of all-cause mortality among survivors of the Great East Japan Earthquake (GEJE).

STUDY DESIGN

Prospective cohort study.

METHODS

We conducted a health survey on 1654 residents aged ≥18 years who lived in two areas affected by the GEJE. One year after the GEJE, between June and August 2012, cognitive SC (helping each other, trust, greeting, and solving problems together) was assessed using a self-administrated questionnaire. We divided the subjects into two groups based on response to questionnaire: "high" or "low." We obtained information on death and emigration from the Residential Registration Record and followed up on the participants from June 2012 to November 2020. The Cox proportional hazards regression analysis was used for estimating the multivariate-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for the risk of all-cause mortality according to each cognitive SC indicator.

RESULTS

During the 8.5 years of follow-up, 213 subjects died (12.9%). For greeting, compared with subjects who were "high," subjects who were "low" were significantly associated with the risk of all-cause mortality (HR: 2.92, 95% CI: 1.19-7.17). No statistically significant association was observed for helping each other, trust, and solving problems together.

CONCLUSION

Our findings suggest that perception of greeting may be associated with the risk of all-cause mortality in survivors after natural disasters.

Abstract P2-13-02: Patient-reported outcomes with trastuzumab monotherapy versus trastuzumab plus standard chemotherapy as a postoperative adjuvant therapy in HER2-positive elderly breast cancer patients (RESPECT): A randomized, open-label, phase 3 clinical trial

OBJECTIVE: The RESPECT trial compared 1-year trastuzumab monotherapy with trastuzumab plus standard chemotherapy as a postoperative adjuvant therapy in HER2-positive elderly breast cancer patients. Primary objective of this study was to verify the noninferiority of 1-year trastuzumab monotherapy to trastuzumab plus chemotherapy in terms of disease free survival, and the planned analysis showed that the difference of restricted mean survival time between two groups at 3 years was 0.45 months (reported by Sawaki at ASCO2018). This report assesses the patients-reported outcomes and health-related quality of life (HRQoL).

PATIENTS AND METHODS: The study was done at 99 hospitals in Japan. Elderly women (70 to 80 years old) with HER2-positive, stageI-IIIA invasive breast cancer treated by surgery with clear resection margins were randomly assigned to receive either 1-year trastuzumab or 1-year trastuzumab plus standard chemotherapy, stratified by age, hormone-receptor status, pathological lymph node metastasis and institution. Patients completed questionnaires at baseline, 2 months, 1year, and 3 years after protocol treatment started. The primary outcome was global HRQoL assessed using Functional Assessment of Cancer Therapy-General (FACT-G) total score, and secondary outcomes were chemotherapy-induced peripheral neuropathy (CIPN), instrumental activities of daily living (IADL), anxiety, depression, and subjective happiness. We did the analyses by intention to treat, including patients who completed questionnaires at baseline before start of protocol treatment, and 5point or more change is meaningful in FACT-G total score. This study is registered with ClinicalTrials.gov, NCT01104935.

RESULTS: Between Oct 2009 and Oct 2014, 275 patients were enrolled in the study, of whom 9 patients were excluded: 135 assigned to trastuzumab monotherapy and 131 assigned to trastuzumab plus chemotherapy. We detected significant difference between treatment groups for: clinically meaningful HRQoL deterioration rate at 2 months (31% for trastuzumab monotherapy vs 48% for trastuzumab plus chemotherapy; p=0.016) and at 1year (19% vs 38%; p=0.009), clinically meaningful HRQoL improvement rate at 2 months (38% for trastuzumab monotherapy vs 15% for trastuzumab plus chemotherapy; p<0.01) and at 1year (43% vs 25%; p=0.021), severe sensory CIPN rate at 2months (1.9% for trastuzumab monotherapy vs 14.4% for trastuzumab plus chemotherapy; p=0.001), IADL score at 1year (11.97 for trastuzumab monotherapy vs 11.54 for trastuzumab plus chemotherapy; p<0.042), Hospital Anxiety and Depression Scale score at 2months (8.92 for trastuzumab monotherapy vs 10.79 for trastuzumab plus chemotherapy; p<0.003), and subjective happiness score at 1year (12.8 for trastuzumab monotherapy vs 11.8 for trastuzumab plus chemotherapy; p<0.024).

CONCLUSION: Given the small advantage of adjuvant trastuzumab plus chemotherapy compared to trastuzumab monotherapy for elderly HER-2 positive breast cancer women, decisions about treatment should be informed by the risk for adverse health effects associated with chemotherapy.

Citation Format: Kobayashi K, Taira N, Sawaki M, Sagawa N, Baba S, Saito T, Kawahara T, Hagiwara Y, Uemura Y, Shimozuma K, Ohashi Y, Mukai H. Patient-reported outcomes with trastuzumab monotherapy versus trastuzumab plus standard chemotherapy as a postoperative adjuvant therapy in HER2-positive elderly breast cancer patients (RESPECT): A randomized, open-label, phase 3 clinical trial [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-13-02.

Abstract P1-11-21: Analysis of cognitive function in elderly HER2-positive breast cancer patients receiving either trastuzumab monotherapy or trastuzumab plus chemotherapy as a postoperative adjuvant treatment: A cognitive function sub-study of a randomized, open-label, phase 3 clinical trial (RESPECT trial)

OBJECTIVE: The effect of trastuzumab(Tmab) or chemotherapy on cognitive function has not been fully understood, especially in elderly breast cancer patients. The RESPECT trial compared 1-year(yr) Tmab monotherapy with Tmab plus standard chemotherapy as adjuvant therapy in elderly patients with HER2-positive breast cancer. The primary objective was to verify the noninferiority of 1-yr Tmab monotherapy compared to Tmab plus chemotherapy in terms of disease-free survival, and the planned analysis showed that the difference of restricted mean survival time between two groups at 3 yrs was 0.45 months (Sawaki at ASCO2018). The goal of this report was to assess the impact of the treatment groups on longitudinal cognitive function.

PATIENTS AND METHODS: The study was performed with patients from 99 hospitals in Japan. Elderly women with HER2-positive, stage I-IIIA invasive breast cancer surgery treated with clear resection margins were randomly assigned to either receive 1-yr Tmab or 1-yr Tmab plus standard chemotherapy. 15 institutions participated in the cognitive sub-study. Cognitive function was assessed using the Mini-Mental State Examination (MMSE) at baseline and at 1 and 3 yrs after treatment. The primary outcome was the amount of change in the MMSE score from the baseline. A linear mixed-effects model was used for comparisons of change in the MMSE score between groups, controlling for time and baseline score. Secondary outcomes were the proportion of both suspected mild dementia (MMSE≤27) and dementia (MMSE≤23) at each time point.

RESULTS: Between October 2009 and October 2014, 275 patients were enrolled in the RESPECT trial, and 57 patients were enrolled in the cognitive function sub-study with 2 patients subsequently excluded. The 55-patient sub-study comprised 29 patients assigned to the Tmab monotherapy group and 26 patients assigned to the Tmab plus chemotherapy group. Primary analysis revealed that change in the MMSE score was not significantly different between the two groups (difference −0.6 at 1 yr and −0.9 at 3 yrs; p=0.136), whereas the baseline score was the only significant factor that had an effect on the amount of change in the MMSE score (p<0.001). The proportions of suspected mild dementia at baseline, and at 1 yr and 3 yrs were 15.4, 32.0, and 41.7% in the Tmab monotherapy group, and 45.8, 17.6, and 28.6% in the Tmab plus chemotherapy group. The proportions of suspected mild dementia at baseline were significantly higher in the Tmab plus chemotherapy group (p=0.04). The proportions of suspected dementia at baseline, and at 1 yr and 3 yrs were 0%, 0%, and 4.2% in the Tmab monotherapy group, and 4.2%, 0%, and 4.8% in the Tmab plus chemotherapy group. There were no significant differences in the proportions of suspected dementia between the treatment groups at each time point.

CONCLUSION: Postoperative chemotherapy for elderly breast cancer patients was considered to have little effect on the onset of dementia during the follow-up period of 3 yrs. Further long-term observation is necessary to obtain a significant conclusion.

Citation Format: Takahashi M, Sawaki M, Hagiwara Y, Uemura Y, Kawahara T, Shimozuma K, Ohashi Y, Saito T, Baba S, Kobayashi K, Mukai H, Taira N. Analysis of cognitive function in elderly HER2-positive breast cancer patients receiving either trastuzumab monotherapy or trastuzumab plus chemotherapy as a postoperative adjuvant treatment: A cognitive function sub-study of a randomized, open-label, phase 3 clinical trial (RESPECT trial) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-11-21.

REVERCE: a randomized phase II study of regorafenib followed by cetuximab versus the reverse sequence for previously treated metastatic colorectal cancer patients

BACKGROUND

The objective of this randomized phase II trial was to evaluate efficacy and safety of the therapeutic sequence of regorafenib followed by cetuximab, compared with cetuximab followed by regorafenib, as the current standard sequence for metastatic colorectal cancer patients.

PATIENTS AND METHODS

Patients with KRAS exon 2 wild-type metastatic colorectal cancer after failure of fluoropyrimidine, oxaliplatin, and irinotecan were randomized to receive sequential treatment with regorafenib followed by cetuximab ± irinotecan (R-C arm), or the reverse sequence [cetuximab ± irinotecan followed by regorafenib (C-R arm)]. The primary end point was overall survival (OS). Key secondary end points included progression-free survival (PFS) with initial treatment (PFS1), PFS with second treatment (PFS2), safety, and quality of life. Exploratory end points included serial biomarker analyses, including oncogenic alterations from circulating tumor DNA or multiple serum or plasma proteins.

RESULTS

One-hundred one patients were randomized and eligible for efficacy analysis. Sequential treatment was successful in 86% patients in both arms. Median OS for R-C and C-R was 17.4 and 11.6 months, respectively (P = 0.0293), with a hazard ratio (HR) of 0.61 for OS [95% confidence interval (CI) 0.39-0.96]. The HR for PFS1 (regorafenib in R-C versus cetuximab in C-R) was 0.97 (95% CI 0.61-1.54), and PFS2 (C in R-C versus R in C-R) was 0.29 (95% CI 0.17-0.50). No unexpected safety signals were observed. The quality of life scores during the entire treatment period was not significantly different between the two arms. Circulating biomarker analyses showed emerging oncogenic alterations in RAS, BRAF, EGFR, HER2, and MET, which were more commonly detected after cetuximab than after regorafenib.

CONCLUSIONS

The therapeutic sequence of regorafenib followed by cetuximab suggests a longer OS than the current standard sequence.

Preoperative oral care and effect on postoperative complications after major cancer surgery

Background

Improving patients' oral hygiene is an option for preventing postoperative pneumonia that may be caused by aspiration of oral and pharyngeal secretions. Whether preoperative oral care by a dentist can decrease postoperative complications remains controversial. A retrospective cohort study was undertaken to assess the association between preoperative oral care and postoperative complications among patients who underwent major cancer surgery.

Methods

The nationwide administrative claims database in Japan was analysed. Patients were identified who underwent resection of head and neck, oesophageal, gastric, colorectal, lung or liver cancer between May 2012 and December 2015. The primary outcomes were postoperative pneumonia and all-cause mortality within 30 days of surgery. Patient background was adjusted for with inverse probability of treatment weighting using propensity scoring.

Results

Of 509 179 patients studied, 81 632 (16·0 per cent) received preoperative oral care from a dentist. A total of 15 724 patients (3·09 per cent) had postoperative pneumonia and 1734 (0·34 per cent) died within 30 days of surgery. After adjustment for potential confounding factors, preoperative oral care by a dentist was significantly associated with a decrease in postoperative pneumonia (3·28 versus 3·76 per cent; risk difference − 0·48 (95 per cent c.i. −0·64 to−0·32) per cent) and all-cause mortality within 30 days of surgery (0·30 versus 0·42 per cent; risk difference − 0·12 (−0·17 to −0·07) per cent).

Conclusion

Preoperative oral care by a dentist significantly reduced postoperative complications in patients who underwent cancer surgery.

In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease

Chagas disease results from infection by Trypanosoma cruzi and is a neglected tropical disease (NTD). Although some treatment drugs are available, their use is associated with severe problems, including adverse effects and limited effectiveness during the chronic disease phase. To develop a novel anti-Chagas drug, we virtually screened 4.8 million small molecules against spermidine synthase (SpdSyn) as the target protein using our super computer “TSUBAME2.5” and conducted in vitro enzyme assays to determine the half-maximal inhibitory concentration values. We identified four hit compounds that inhibit T. cruzi SpdSyn (TcSpdSyn) by in silico and in vitro screening. We also determined the TcSpdSyn–hit compound complex structure using X-ray crystallography, which shows that the hit compound binds to the putrescine-binding site and interacts with Asp171 through a salt bridge.

Long-term health status as measured by EQ-5D among patients with metastatic breast cancer: comparison of first-line oral S-1 and taxane therapies in the randomized phase III SELECT BC trial

Purpose

The goal of chemotherapy for metastatic breast cancer (MBC) is to prolong survival and maintain health-related quality of life. This study aimed to evaluate long-term health status of patients with MBC who participated in the phase III randomized SELECT BC trial.

Methods

In the SELECT BC trial, patients were randomly allocated to the S-1 or taxane (paclitaxel or docetaxel) arm. Health status was assessed by EQ-5D at pre-treatment, 3 and 6 months after randomization, and every 6 months thereafter to the extent possible. Least square mean scores were assessed to compare EQ-5D index values between groups. Time to deterioration analysis was also performed by defining the minimally important difference of EQ-5D as 0.05 or 0.1.

Results

The number of patients for EQ-5D analysis was 175 and 208 in the taxane and S-1 arms, respectively. Least square mean EQ-5D index values up to 60 months were 0.741 (95 % CI [0.713–0.769]) in the taxane arm and 0.748 [0.722–0.775] in the S-1 arm. The EQ-5D index value during PFS up to 12 months in the S-1 was superior to the corresponding index value in the taxane (0.812 [0.789–0.834] vs. 0.772 [0.751–0.792], P = 0.009). Time to deterioration analysis also revealed that S-1 significantly delayed the deterioration of EQ-5D index value during the period before progression (P = 0.002 and 0.003).

Conclusions

Our findings suggest that the EQ-5D index value was higher in patients treated with S-1 during first-line chemotherapy. Considering non-inferiority of S-1 in terms of OS, obtained quality-adjusted life years may be greater in the S-1 arm.

Fixation stability dictates the differentiation pathway of periosteal progenitor cells in fracture repair

This study compared fracture repair stabilized by intramedullary pin (IMP) or external fixation (EF) in GFP reporter mice. A modified IMP was used as control while EF utilized six needles inserted transversely through the tibia and into a segment of a syringe barrel. X-rays taken at days 0, 14, and 35 showed that IMP resulted in significant three-dimensional deformity with a large callus while EF showed minimal deformity and callus formation. Cryohistological analysis of IMP at day 14 confirmed a large ColX-RFPchry+ callus surrounded by woven bone (Col3.6-GFPcyan) and TRAP+ osteoclasts with mature bone (hOC-GFPtpz) at the base. By day 35, cartilaginous components had been resorbed and an outer cortical shell (OCS) showed evidence of inward modeling. In contrast, the EF at day 14 showed no evidence of cartilage formation. Instead, periosteal-derived osteoblasts (Col3.6-GFPcyan) entered the fracture cleft and formed woven bone that spanned the marrow space. By day 35, mature bone had formed that was contiguous with the opposing cortical bone. Fracture site stability greatly affects the cellular response during repair and must be considered in the preclinical models that test therapies for improving fracture healing.

Response of knee fibrocartilage to joint destabilization

OBJECTIVE

A major challenge to understanding osteoarthritis (OA) pathology is identifying the cellular events that precede the onset of cartilage damage. The objective of this study is to determine the effect of joint destabilization on early changes to fibrocartilage in the joint.

DESIGN/METHODS

The anterior cruciate ligament was transected in collagen reporter mice (Col1CFP and ColXRFP). Mineralization labels were given every 2 weeks to measure new mineralized cartilage apposition. Novel fluorescent histology of mineralized tissue was used to characterize the changes in fibrocartilage at 2 and 4 weeks post-injury.

RESULTS

Changes in fibrocartilaginous structures of the joint occur as early as 2 weeks after injury and are well developed by 4 weeks. The alterations are seen in multiple entheses and in the medial surface of the femoral and tibial condyles. In the responding entheses, mineral apposition towards the ligament midsubstance results in thickening of the mineralize fibrocartilage. These changes are associated with increases in ColX-RFP, Col1-CFP reporter activity and alkaline phosphatase enzyme activity. Mineral apposition also occurs in the fibrocartilage of the non-articular regions of the medial condyles by 2 weeks and develops into osteophytes by 4 weeks post-injury. An unexpected observation is punctate expression of tartrate resistant acid phosphatase activity in unmineralized fibrochondrocytes adjacent to active appositional mineralization.

DISCUSSION

These observations suggest that fibrocartilage activates prior to degradation of the articular cartilage. Thus clinical and histological imaging of fibrocartilage may be an earlier indicator of disease initiation and may indicate a more appropriate time to start preventative treatment.

Effects of professional oral health care on elderly: randomized trial

OBJECTIVE

To better understand the role of the professional oral health care for elderly in improving geriatric oral health, the effects of short-term professional oral health care (once per week for 1 month) on oral microbiological parameters were assessed.

METHODS

Parallel, open-labelled, randomize-controlled trial was undertaken in a nursing home for elderly in Shizuoka, Japan. Thirty-four dentate elderly over 74 years were randomly assigned from ID number to the intervention (17/34) and control (17/34) groups. The outcomes were changes in oral microbiological parameters (number of bacteria in unstimulated saliva; whole bacteria, Streptococcus, Fusobacterium and Prevotella: opportunistic pathogens detection: and index of oral hygiene evaluation [Dental Plaque Index, DPI]) within the intervention period. Each parameter was evaluated at before and after intervention period. Four elderly were lost from mortality (1), bone fracture (1), refused to participate (1) and multi-antibiotics usage (1). Finally, 30 elderly were analysed (14/intervention and 16/control).

RESULTS

At baseline, no difference was found between the control and intervention groups. After the intervention period, the percentage of Streptococcus species increased significantly in the intervention group (Intervention, 86% [12/14]; Control, 50% [8/16]: Fisher's, right-tailed, P < 0.05). Moreover, DPI significantly improved in the intervention group (Intervention, 57% [8/14]; Control, 13% [2/16]: Fisher's, two-tailed, P < 0.05). The improvement in DPI extended for 3 months after intervention. None of side effects were reported.

CONCLUSION

The short-term professional oral health care can improve oral conditions in the elderly.

Accelerating quantum chemistry calculations with graphical processing units - toward in high-density (HD) silico drug discovery

The growing power of central processing units (CPU) has made it possible to use quantum mechanical (QM) calculations for in silico drug discovery. However, limited CPU power makes large-scale in silico screening such as virtual screening with QM calculations a challenge. Recently, general-purpose computing on graphics processing units (GPGPU) has offered an alternative, because of its significantly accelerated computational time over CPU. Here, we review a GPGPU-based supercomputer, TSUBAME2.0, and its promise for next generation in silico drug discovery, in high-density (HD) silico drug discovery.

Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists

INTRODUCTION

G protein-coupled receptors (GPCRs) are integral membrane proteins which contain seven-transmembrane-spanning alpha-helices. GPCR-mediated signaling has been associated with various human diseases, positioning GPCRs as attractive targets in the drug discovery field. Recently, through advances in protein engineering and crystallography, the number of resolved GPCR structures has increased dramatically. This growing availability of GPCR structures has greatly accelerated structure-based drug design (SBDD) and in silico screening for GPCR-targeted drug discovery.

AREAS COVERED

The authors introduce the current status of X-ray crystallography of GPCRs and what has been revealed from the resolved crystal structures. They also review the recent advances in SBDD and in silico screening for GPCR-targeted drug discovery and discuss a docking study, using homology modeling, with the discovery of potent antagonists of the vasopressin 1b receptor.

EXPERT OPINION

Several innovative protein engineering techniques and crystallographic methods have greatly accelerated SBDD, not only for already-resolved GPCRs but also for those structures which remain unclear. These technological advances are expected to enable the determination of GPCR-fragment complexes, making it practical to perform fragment-based drug discovery. This paves the way for a new era of GPCR-targeted drug discovery.

Unidirectional Mechanistic Valved Mechanisms for Ammonia Transport in GatCAB

Glutamine amidotransferase CAB (GatCAB), a crucial enzyme involved in translational fidelity, catalyzes three reactions: (i) the glutaminase reaction to yield ammonia (NH3 or NH4(+)) from glutamine, (ii) the phosphorylation of Glu-tRNA(Gln), and (iii) the transamidase reaction to convert the phosphorylated Glu-tRNA(Gln) to Gln-tRNA(Gln). In the crystal structure of GatCAB, the two catalytic centers are far apart, and the presence of a hydrophilic channel to transport the molecules produced by the reaction (i) was proposed. We investigated the transport mechanisms of GatCAB by molecular dynamics (MD) simulations and free energy (PMF) calculations. In the MD simulations (in total ∼1.1 μs), the entrance of the previously proposed channel is closed, as observed in the crystal structure. Instead, a novel hydrophobic channel has been identified in this study: Since the newly identified entrance opened and closed repeatedly in the MD simulations, it may act as a gate. The calculated free energy difference revealed the significant preference of the newly identified gate/channel for NH3 transport (∼10(4)-fold). In contrast, with respect to NH4(+), the free energy barriers are significantly increased for both channels due to tight hydrogen-bonding with hydrophilic residues, which hinders efficient transport. The opening of the newly identified gate is modulated by Phe206, which acts as a "valve". For the backward flow of NH3, our PMF calculation revealed that the opening of the gate is hindered by Ala207, which acts as a mechanistic "stopper" against the motion of the "valve" (Phe206). This is the first report to elucidate the detailed mechanisms of unidirectional mechanistic valved transport inside proteins.

Brain localization of leucine-rich α2-glycoprotein and its role

OBJECTIVES

We have previously reported that the level of leucine-rich alpha-2-glycoprotein (LRG) expression is specifically increased in cerebrospinal fluid (CSF) of idiopathic normal pressure hydrocephalus (INPH). The objective of this study is to examine the localization of LRG - the cerebral areas where it is expressed.

METHOD

The histological sections of autopsied brain specimens from ten subjects, five adult cases (mean age 43.6 years; range 34-50 years) and five senile cases (mean age 76.0 years; range 67-88 years) were prepared, multistained with antibodies against human LRG, glial fibrillary acidic protein (GFAP), CD31, and aquaporin-4 (AQP4), and reviewed for the expression sites of LRG.

RESULTS

Immunostains of GFAP and LRG were compared in standard brain specimens from elderly patients. The results indicated that LRG is distributed throughout the entire brain, with especially high expression in the deep cerebral cortex. In addition, the cells that express LRG showed similar morphology to astrocytes. Double staining of CD31 and LRG revealed a significant expression of LRG in the pericapillary regions. The expression was observed in resident astrocytes, as well as in the capillary vessel to which astrocytic processes grow and adhere. When age-related comparisons were made between senile and adult specimens, LRG expression increased with age.

CONCLUSION

LRG expression in resident astrocytes increased with age.

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems.

Intradermal delivery of recombinant vaccinia virus vector DIs induces gut-mucosal immunity

Antigen-specific mucosal immunity is generally induced by the stimulation of inductive mucosal sites. In this study, we found that the replication-deficient vaccinia virus vector, DIs, generates antigen-specific mucosal immunity and systemic responses. Following intradermal injection of recombinant DIs expressing simian immunodeficiency virus gag (rDIsSIVgag), we observed increased levels of SIV p27-specific IgA and IgG antibodies in faecal extracts and plasma samples, and antibody-forming cells in the intestinal mucosa and spleen of C57BL/6 mice. Antibodies against p27 were not detected in nasal washes, saliva, and vaginal washes. The enhanced mucosal and systemic immunity persisted for 1 year of observation. Induction of Gag-specific IFN-gamma spot-forming CD8(+) T cells in the spleen, small intestinal intraepithelial lymphocytes, and submandibular lymph nodes was observed in the intradermally injected mice. Heat-inactivated rDIsSIVgag rarely induced antigen-specific humoral and T-helper immunity. Moreover, rDIsSIVgag was detected in MHC class II IA antigen-positive (IA(+)) cells at the injection site. Consequently, intradermal delivery of rDIs effectively induces antigen-specific humoral and cellular immunity in gut-mucosal tissues of mice. Our data suggest that intradermal injection of an rDIs vaccine may be useful against mucosally transmitted pathogens.

Editing mechanism of aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst

Aminoacyl-tRNA synthetases (aaRSs) are critical for the translational process, catalyzing the attachment of specific amino acids to their cognate tRNAs. To ensure formation of the correct aminoacyl-tRNA, and thereby enhance the reliability of translation, several aaRSs have an editing capability that hinders formation of misaminoacylated tRNAs. We investigated theoretically the mechanism of the editing reaction for a class I enzyme, leucyl-tRNA synthetase (LeuRS), complexed with a misaminoacylated tRNA(Leu), employing ab initio hybrid quantum mechanical/molecular mechanical potentials in conjunction with molecular dynamics simulations. It is shown that the water molecule that acts as the nucleophile in the editing reaction is activated by a 3'-hydroxyl group at the 3'-end of tRNA(Leu) and that the O2' atom of the leaving group of the substrate is capped by one of the water's hydrogen atoms. Thus, it is shown that editing is a self-cleavage reaction of the tRNA and so it is the tRNA, and not the protein, that drives the reaction. The protein does, however, have an important stabilizing effect on some high-energy intermediates along the reaction path, which is more efficient than the ribozyme would be alone. This indicates that editing is achieved by a novel "hybrid ribozyme/protein catalyst". Analysis of existing experimental data and additional modeling shows that this ribozymal mechanism appears to be widespread, occurring in the ribosome as well as in other aaRSs. It also suggests transitional forms that could have played an important role in the RNA world hypothesis for the origin of life.

Modulation of electronic structures of bases through DNA recognition of protein

The effects of environmental structures on the electronic states of functional regions in a fully solvated DNA·protein complex were investigated using combined ab initio quantum mechanics/molecular mechanics calculations. A complex of a transcriptional factor, PU.1, and the target DNA was used for the calculations. The effects of solvent on the energies of molecular orbitals (MOs) of some DNA bases strongly correlate with the magnitude of masking of the DNA bases from the solvent by the protein. In the complex, PU.1 causes a variation in the magnitude among DNA bases by means of directly recognizing the DNA bases through hydrogen bonds and inducing structural changes of the DNA structure from the canonical one. Thus, the strong correlation found in this study is the first evidence showing the close quantitative relationship between recognition modes of DNA bases and the energy levels of the corresponding MOs. Thus, it has been revealed that the electronic state of each base is highly regulated and organized by the DNA recognition of the protein. Other biological macromolecular systems can be expected to also possess similar modulation mechanisms, suggesting that this finding provides a novel basis for the understanding for the regulation functions of biological macromolecular systems.

Functional roles of a structural element involving Na+-pi interactions in the catalytic site of T1 lipase revealed by molecular dynamics simulations

Interactions between metal ions and pi systems (metal-pi interactions) are known to confer significant stabilization energy. However, in biological systems, few structures with metal-pi coordination have been determined; thus, its roles must still be elucidated. The cation-pi interactions are not correctly described by current molecular mechanics even when using a polarizable force field, and thus they require quantum mechanical calculations for accurate estimation. However, the huge computational costs of the latter methodologies prohibit long-time molecular dynamics (MD) simulations. Accordingly, we developed a novel scheme to obtain an effective potential for calculating the interaction energy with an accuracy comparable to that of advanced ab initio calculations at the CCSD(T) levels, and with computational costs comparable to those of conventional MM calculations. Then, to elucidate the functional roles of the Na(+)-phenylalanine (Phe) complex in the catalytic site of T1 lipase, we performed MD simulations in the presence/absence of the accurate Na(+)-pi interaction energy. A comparison of these MD simulations revealed that a significantly large enthalpy gain in Na(+)-Phe16 substantially stabilizes the catalytic site, whereas a water molecule could not be substituted for Na(+) for sufficient stabilization energy. Thus, the cation-pi interaction in the lipase establishes a remarkably stable core structure by combining a hydrophobic aromatic ring and hydrophilic residues, of which the latter form the catalytic triad, thereby contributing to large structural changes from the complex with ligands to the free form of the lipase. This is the first report to elucidate the detailed functional mechanisms of Na(+)-pi interactions.

A novel computational scheme for accurate and efficient evaluation of π-π and π-σ stacking

Stacking involving aromatic rings has a significant contribution to the structural stability of biological macromolecules. However, conventional calculations such as density functional theory (DFT) and molecular mechanics (MM) fail to estimate such stabilization energies, most of which are fundamentally derived from van der Waals interactions. For the accurate description, higher level ab initio calculations, such as CCSD(T), should be employed; however, their computational costs are huge. MM calculations provide better estimation of the interactions of the aromatic rings than DFT, but not sufficient. In this report, we propose a novel scheme to calculate the interaction energy at an accuracy compatible to CCSD(T) with the computational costs comparable to MM calculations. In our scheme, the electron density of the aromatic rings is represented by Gaussian-type functions, and the parameters involved in the functions are determined by an optimization scheme to reproduce the CCSD(T) results. Here, we employ model structures involving tryptophan and tyrosine rings, and successfully obtain the optimal parameter set. By using this type of representation of the stacking proposed, the computational time to calculate the interaction energy is dramatically reduced by 10(-10)-fold, compared with CCSD(T).

QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines

An interface program connecting a quantum mechanics (QM) calculation engine, GAMESS, and a molecular mechanics (MM) calculation engine, AMBER, has been developed for QM/MM hybrid calculations. A protein-DNA complex is used as a test system to investigate the following two types of QM/MM schemes. In a 'subtractive' scheme, electrostatic interactions between QM/MM regions are truncated in QM calculations; in an 'additive' scheme, long-range electrostatic interactions within a cut-off distance from QM regions are introduced into one-electron integration terms of a QM Hamiltonian. In these calculations, 338 atoms are assigned as QM atoms using Hartree-Fock (HF)/density functional theory (DFT) hybrid all-electron calculations. By comparing the results of the additive and subtractive schemes, it is found that electronic structures are perturbed significantly by the introduction of MM partial charges surrounding QM regions, suggesting that biological processes occurring in functional sites are modulated by the surrounding structures. This also indicates that the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of biological macromolecules.

Electronic and geometric structures of the blue copper site of azurin investigated by QM/MM hybrid calculations

The electronic and geometric structures of the copper-binding site in a fully solvated azurin were investigated using quantum mechanics (QM) and molecular mechanics (MM) hybrid calculations. Two types of computational models were applied to evaluate the effects of the environment surrounding the active site. In model I, long-distance electrostatic interactions between QM region atoms and partial point charges of the surrounding protein moieties and solvent water were calculated in a QM Hamiltonian, for which the spin-unrestricted Hartree-Fock (UHF)/density functional theory (DFT) hybrid all-electron calculation with the B3LYP functional was adopted. In model II, the QM Hamiltonian was not allowed to be polarized by those partial point charges. Models I and II provided different descriptions of the copper coordination structure, particularly for the coordinative bonds including a large dipole. In fact, the Cu-O(Gly45) and Cu-S(Cys112) bonds are sensitive to the treatment of long-distance electrostatic interactions in the QM Hamiltonian. This suggests that biological processes occurring in the active site are regulated by the surrounding structures of protein and solvent, and therefore the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of the copper active site of metalloenzymes.

Evaluation of stabilization energies in π-π and cation-π interactions involved in biological macromolecules by ab initio calculations

Non-covalent interactions involving aromatic rings contribute significantly to the stability of three-dimensional structures of biological macromolecules. Therefore, accurate descriptions of such interactions are crucial in understanding the functional mechanisms of biological molecules. However, it is also well known that, for some cases where van der Waals interactions make a dominant contribution, conventional ab initio electronic structure calculations, such as density functional theory, do not produce accurate interaction energies. In this study, we evaluated molecular mechanics (MM) calculations for two types of interactions involving aromatic rings, π-π interactions and cation-π interactions, by comparing our results with those obtained by advanced ab initio calculations at the coupled-cluster with singles, doubles and perturbative triples level. In structures with stacked aromatic rings, interaction energies obtained by MM calculations are overestimated. On the other hand, for cation-π interactions, the energies in MM calculations are significantly underestimated. In both cases, addition of an induction energy based on polarization effects also fails to improve the estimate given by MM calculations. The results indicate that current effective pairwise potentials are inappropriate to represent π-π and cation-π interactions.