In Silico Design of Natural Inhibitors of ApoE4 from the Plant Moringa oleifera: Molecular Docking and Ab Initio Fragment Molecular Orbital Calculations

Alzheimer's disease (AD) is a neurological disease, and its signs and symptoms appear slowly over time. Although current Alzheimer's disease treatments can alleviate symptoms, they cannot prevent the disease from progressing. To accurately diagnose and treat Alzheimer's disease, it is therefore necessary to establish effective methods for diagnosis. Apolipoprotein E4 (ApoE4), the most frequent genetic risk factor for AD, is expressed in more than half of patients with AD, making it an attractive target for AD therapy. We used molecular docking simulations, classical molecular mechanics optimizations, and ab initio fragment molecular orbital (FMO) calculations to investigate the specific interactions between ApoE4 and the naturally occurring compounds found in the plant Moringa Oleifera. According to the FMO calculations, quercetin had the highest binding affinity to ApoE4 among the sixteen compounds because its hydroxyl groups generated strong hydrogen bonds with the ApoE4 residues Trp11, Asp12, Arg15, and Asp130. As a result, we proposed various quercetin derivatives by introducing a hydroxyl group into quercetin and studied their ApoE4 binding properties. The FMO data clearly showed that adding a hydroxyl group to quercetin improved its binding capacity to ApoE4. Furthermore, ApoE4 Trp11, Asp12, Arg15, and Asp130 residues were discovered to be required for significant interactions between ApoE4 and quercetin derivatives. They had a higher ApoE4 binding affinity than our previously proposed epicatechin derivatives. Accordingly, the current results evaluated using the ab initio FMO method will be useful for designing potent ApoE4 inhibitors that can be used as a candidate agent for AD treatment.

Proposal of novel ApoE4 inhibitors from the natural spice Cinnamon for the treatment of Alzheimer's disease: Ab initio molecular simulations

Alzheimer's disease (AD), one of the most common neurodegenerative diseases, is a major factor contributing to cognitive impairment in older adults. Current therapeutic treatments can only relieve the symptoms of AD, but they cannot stop the progression of the disease because it takes a long time for clinical symptoms to manifest. Therefore, it is essential to develop effective diagnostic strategies for early detection and treatment of AD. As the most common genetic risk factor for AD, apolipoprotein E4 (ApoE4) is present in more than half of patients with AD, and it can be a target protein for AD therapy. We used molecular docking, classical molecular mechanics optimizations, and ab initio fragment molecular orbital (FMO) calculations to investigate the specific interactions between ApoE4 and Cinnamon-derived compounds. Of the 10 compounds, epicatechin was found to have the highest binding affinity to ApoE4 because the hydroxyl groups of epicatechin form strong hydrogen bonds with the Asp130 and Asp12 residues of ApoE4. Therefore, we proposed some epicatechin derivatives by adding a hydroxyl group to epicatechin and studied their interactions with ApoE4. The FMO results indicate that the addition of a hydroxyl group to epicatechin increases its binding affinity to ApoE4. It is also revealed that the Asp130 and Asp12 residues of ApoE4 are important for the binding between ApoE4 and the epicatechin derivatives. These findings will help propose potent inhibitors against ApoE4, leading to a proposal for effective therapeutic candidates for AD.

Structure-based drug design of novel M. tuberculosis InhA inhibitors based on fragment molecular orbital calculations

2-trans enoyl-acyl carrier protein reductase (InhA) is a promising target for developing novel chemotherapy agents for tuberculosis, and their inhibitory effects on InhA activity were widely investigated by the physicochemical experiments. However, the reason for the wide range of their inhibitory effects induced by similar agents was not explained by only the difference in their chemical structures. In our previous molecular simulations, a series of heteroaryl benzamide derivatives were selected as candidate inhibitors against InhA, and their binding properties with InhA were investigated to propose novel derivatives with higher binding affinity to InhA. In the present study, we extended the simulations for a series of 4-hydroxy-2-pyridone derivatives to search widely for more potent inhibitors against InhA. Using ab initio fragment molecular orbital (FMO) calculations, we elucidated the specific interactions between InhA residues and the derivatives at an electronic level and highlighted key interactions between InhA and the derivatives. The FMO results clearly indicated that the most potent inhibitor has strong hydrogen bonds with the backbones of Tyr158, Thr196, and NADH of InhA. This finding may provide informative structural concepts for designing novel 4-hydroxy-2-pyridone derivatives with higher binding affinity to InhA. Our previous and present molecular simulations could provide important guidelines for the rational design of more potent InhA inhibitors.

Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: molecular docking and ab initio fragment molecular orbital calculations

The novel coronavirus 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly worldwide, and new drug treatments for COVID-19 are urgently required. To find the potential inhibitors against the main protease (Mpro) of SARS-CoV-2, we investigated the inhibitory potential of naturally occurring compounds from the plants Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis, using molecular docking, classical molecular mechanics optimizations, and ab initio fragment molecular orbital (FMO) calculations. Of the 35 compounds that we simulated, feralolide from Aloe vera exhibited the highest binding affinity against Mpro. Therefore, we proposed novel compounds based on the feralolide and investigated their binding properties to Mpro. The FMO results indicated that the introduction of a hydroxyl group into feralolide significantly enhances its binding affinity to Mpro. These results provide useful information for developing potent Mpro inhibitors.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

POS0728 ASSOCIATION BETWEEN TREATMENT GOAL ACHIEVEMENT AND GRIT PERSONALITY CHARACTERISTICS OF ATTENDING PHYSICIAN IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS: A MULTICENTER CROSS-SECTIONAL STUDY

Background

In clinical practice for systemic lupus erythematosus (SLE), the concept of “treat to target” has been introduced with an established goal of reducing glucocorticoid dose as much as possible while controlling disease activity. Although it has been shown that various personality characteristics of patients with SLE affect their disease activity and damage, it is not clear whether the personality characteristics of attending physicians affect the outcomes of patients with SLE. Grit is a personality trait characterized by perseverance and passion for achieving long-term goals.

Objectives

This study aims to evaluate the relationship between attending physicians’ grit personality characteristics and treatment goal achievements in patients with SLE.

Methods

A cross-sectional study was conducted on 386 patients with SLE in five referral hospitals in Japan. The main exposure was the “perseverance” and “consistency” (scores 1-5) of the attending physicians, as measured by the Short Grit Scale, and the primary outcome was the achievement of the Lupus Low Disease Activity Score (LLDAS). Considering the clustering of achievement of LLDAS by each attending physician, the association between attending physician’s personality and LLDAS was analyzed by logistic regression with cluster robust variance estimation. Odds ratios to assess the relationship between perseverance and consistency and LLDAS were estimated with adjustment for confounders (age, sex, disease duration, hydroxychloroquine use, immunosuppressant use, and Systemic Lupus International Collaborating Clinics-Damage Index). We used multiple imputation to handle the uncertainty caused by missing values of potential confounders on the assumption of missing at random.

Results

The median age of the patients was 45 years (interquartile range[IQR],36-56), 88% were female, and the median disease duration was 152 months(IQR, 80-240). Thirty-seven doctors were in charge of the patients (1-79 patients/each doctor). The median age of the attending physicians was 40 years (IQR, 35-43), and 19% were female. The median perseverance and consistency scores of attending physicians were 3.1 (IQR, 3.0-3.5) and 3.3 (IQR, 2.8-3.8), respectively. Of the enrolled patients, 154 (40%) had achieved LLDAS. The attending physicians with a lower consistency score of <3 were more frequent in the patients who achieved LLDAS (40% vs. 29%, p=0.026). The lower consistency score of attending physicians was still related to LLDAS independently (adjusted odds ratio 1.63, 95% confidential interval 1.17-2.27). There was no association between the achievement of LLDAS and perseverance.

Conclusion

The grit personality characteristics of the attending physician may affect the achievement of treatment goals in patients with SLE.

Disclosure of Interests

KEN-EI SADA Speakers bureau: I received speaker’s fees from Glaxo Smith Kline K.K., Grant/research support from: I received a research grant from Pfizer Inc., Yoshia Miyawaki: None declared, Kenta Shidahara: None declared, Shoichi Nawachi: None declared, Yu Katayama: None declared, Yosuke ASANO: None declared, Keigo Hayashi: None declared, Keiji Ohashi: None declared, Eri Katsuyama: None declared, Takayuki Katsuyama: None declared, Mariko Narazaki: None declared, Yoshinori Matsumoto: None declared, Nao Oguro: None declared, Yuichi Ishikawa: None declared, Natsuki Sakurai: None declared, Chiharu Hidekawa: None declared, Ryusuke Yoshimi: None declared, Takanori Ichikawa: None declared, Dai Kishida: None declared, Yasuhiro Shimojima: None declared, Noriaki Kurita: None declared, Nobuyuki Yajima: None declared

POS1404 SHARED DECISION MAKING AND INTERNET USE FOR GATHERING HEALTH INFORMATION IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS: A MULTICENTER CROSS-SECTIONAL STUDY

Background

It is well known that providing appropriate health information to patients with systemic lupus erythematosus (SLE) has an advantage in the treatment decision making process. In modern information society the growing popularity of smartphones and social networking services, patients have more access to online health information. However, there are concerns that Internet use may inversely affect the shared decision making (SDM) process with their attending physicians if they receive inaccurate information.

Objectives

This study aimed to investigate how online information gathering behavior affects SDM with their attending physicians.

Methods

In this cross-sectional study, information of 386 patients with SLE, which were enrolled from five Japanese institutions between June 2020 and August 2021, were analyzed. The main exposure was time spent on the Internet per day (excluding time used for working). It was divided into four categories (none, <1 hour, 1-2 hours, > 2 hours). Patients were asked to select the source of health care information they would like to access first and were categorized into physicians, the Internet, and other media sources (family and friends, healthcare professionals other than physicians, or TV and radio, etc.). Outcome was shared decision making measured via the 9-item Shared Decision Making Questionnaire (SDM-Q-9 [scores 0-100]). To assess the relationship between the time of Internet use and SDM, we fitted general linear models adjusted for age, gender, education level, household income, marital status, history of cancer, disease duration, and disease activity. Chained equations were used to impute missing values of covariates.

Results

This study ultimately employed 334 patients whose mean age and female ratio were 45.3 years (standard deviation 13.8) and 87.7%, respectively. 68.9% of the patients indicated that they would like to access their physicians first, and 19.5% indicated that they would like to access the Internet first. Compared to patients who chose their physician as their first access to health information, there was no difference in SDM-Q-9 among patients who chose the Internet, but patients who chose other media had significantly lower SDM-Q-9 (-7.7 point, 95% confident interval [CI] -14.4 to -0.92, P=0.026). Besides, SDM-Q-9 scores were significantly lower in patients who did not use the Internet compared to those who used it for more than two hours except for their work activities (-9.6, 95%CI -18.9 to -0.26, P=0.044).

Conclusion

The present study suggests that SDM between physicians and patients is positively rather than adversely associated with online information-gathering behavior. Rheumatologists also need to be aware that how patients prefer to access health information to establish a good physician-patient relationship for SDM. In addition, rheumatologists may need to introduce their patients to websites offering appropriate health information.

Disclosure of Interests

None declared

AB0474 IMPACT OF HEALTH LITERACY ON TRUST IN PHYSICIANS AMONG PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS: THE TRUMP2-SLE PROJECT

Background

Information technology has expanded the gap in patient health literacy (HL), and HL has various implications on the trust in patient-doctor relationship. Previously, only functional HL, the ability to interpret health information through reading and writing skills, has been studied in patients with SLE (1).

Objectives

We examined how trust in physicians is affected by the broader concept of HL, including communicative HL, the ability to extract health information from communication to use, and critical HL, the ability to discern and use such information (2).

Methods

This cross-sectional study enrolled 362 SLE patients at 5 sites between June 2020 and August 2021. Three domains of HL (i.e., functional HL, communicative HL, and critical HL) were assessed using the 14-item FCCHL scale (range: 1-4 points for each domain). The outcomes were patients’ trust in their physicians and physicians in general and were measured using the Japanese version of the 5-item Wake Forest Physician Trust scales (range: 0-100 points for each scale). General linear models adjusted for age, gender, education, income, SLEDAI, disease duration, depression, and hours of Internet use were conducted. Subsequently, a series of general linear models were then fit to each of the three domains of HL to examine whether or not it was associated with the aforementioned covariates.

Results

The median age of the patients was 45 (interquartile range [IQR],34-55), 88% were female. The median value of SLEDAI was 4 ([IQR], 2-8), Trust in one’s physician was 80 ([IQR], 70-95) and trust in physicians generally was 65 ([IQR], 50-80). Trust in one’s physician increased with higher functional and communicative HL (per 1-pt increase, 3.2 [95%CI 0.7 to 5.9]; 5.4 [95%CI 1.6 to 9.3]). Trust in doctors generally increased with higher communicative HL and decreased with higher critical HL (per 1-pt increase, 6.8 [95% CI 2.0 to 12]; -6.7 [95% CI -12 to -1.9]). Lower functional HL was associated with older age and depression, while higher HL was associated with higher educational level. Higher communicative HL and critical HL were each associated with longer Internet use.

Conclusion

In patients with SLE, higher trust in one’s physician was associated with both functional and communicative HL, while higher trust in physicians generally was associated with higher communicative HL and lower critical HL. Our findings suggest that trusting relationships may be fostered by the encouragement of rheumatologists to cultivate patients’ ability to share their health problems with their physicians and family members and to obtain useful health information (i.e., communicative HL), rather than to improve their ability to discern health information (i.e., critical HL).

References

[1]Maheswaranathan M, Cantrell S, Eudy AM, Rogers JL, Clowse MEB, Hastings SN, et al. Investigating Health Literacy in Systemic Lupus Erythematosus: a Descriptive Review. Curr Allergy Asthma Rep. 2020;20(12):79.

[2]Ishikawa H, Takeuchi T, Yano E. Measuring functional, communicative, and critical health literacy among diabetic patients. Diabetes Care. 2008;31(5):874-9.

Disclosure of Interests

Nao Oguro: None declared, Nobuyuki Yajima: None declared, Yoshia Miyawaki: None declared, Ryusuke Yoshimi: None declared, Yasuhiro Shimojima: None declared, KEN-EI SADA Speakers bureau: He received speaker’s fees from Glaxo Smith

Kline K.K., Grant/research support from: He received a research grant from Pfizer Inc.,, Keigo Hayashi: None declared, Kenta Shidahara: None declared, Natsuki Sakurai: None declared, Chiharu Hidekawa: None declared, Dai Kishida: None declared, Takanori Ichikawa: None declared, Yuichi Ishikawa: None declared, Noriaki Kurita: None declared

Specific interactions between the alkaline protease of P. aeruginosa and its natural peptide inhibitor: ab initio molecular simulations

Alkaline protease aeruginolysin (APR) is an important virulence factor in the evasion of the immune system by Pseudomonas aeruginosa (P. aeruginosa). The P. aeruginosa genome also encodes the highly potent and specific APR peptide inhibitor (APRin). However, the structural reason for the significant inhibition has not been revealed. Using ab initio molecular simulations, we here investigated the specific interactions between APR and APRin to elucidate which amino acid residues of APRin and APR contribute strongest to the inhibition. Since APR has a Zn²⁺ ion at the ligand-binding site and histidine and glutamic acid residues are coordinated with Zn²⁺, it is essential to precisely describe these coordination bonds to elucidate the specific interactions between APR and APRin. Therefore, we employed the ab initio fragment molecular orbital method to investigate the specific interactions at an electronic level. The results revealed that Ser1 and Ser2 at the N-terminus of APRin significantly contribute to the binding between APRin and APR. In particular, Ser1 binds strongly to Zn²⁺ as well as to the sidechains of His176(Hid), His180(Hid), and His186(Hid) in APR. This is the main reason for the strong interaction between APR and APRin. The results also elucidated significant contributions of the positively charged Arg83 and Arg90 residues of APRin to the binding with APR. These findings may provide information useful for the design of novel small agents as potent APR inhibitors.

Proposal of selective inhibitor for bacterial zinc metalloprotease: Molecular mechanics and ab initio molecular orbital calculations

The zinc metalloprotease pseudolysin (PLN) secreted from Pseudomonas aeruginosa degrades extracellular proteins to produce bacterial nutrition, and various types of PLN inhibitors have been developed to suppress the bacterial growth. However, as the structure of the ligand-binding pocket of PLN has large similarities to those of human matrix metalloproteinases (MMPs) and other human zinc metalloprotease, there is a risk that PLN inhibitors also inhibit human zinc proteases. In this study, we propose a novel agent that may bind stronger to PLN than to MMPs. The compound is proposed based on the specific molecular interactions between existing agents and PLN/MMP metalloproteases evaluated by the present molecular simulations. First, we confirmed that the binding energies of PLN agents evaluated using the ab initio fragment molecular orbital method were comparable to the IC₅₀ values obtained through previous experiments. In addition, the specific molecular interactions between these agents and MMP-9 were investigated to elucidate the fact that some of the agents bind weaker to MMP than PLN. Based on the results, we proposed a novel agent having a succinimide group introduce by a hydroxamic acid group and investigated its binding properties with PLN and MMP. The results may provide useful information for the development of potent inhibitors for PLN with few potential side effects in human bodies.

Half-integer quantized anomalous thermal Hall effect in the Kitaev material candidate α-RuCl3

Half-integer thermal quantum Hall conductance has recently been reported for the two-dimensional honeycomb material α-RuCl₃ We found that the half-integer thermal Hall plateau appears even for a magnetic field with no out-of-plane components. The measured field-angular variation of the quantized thermal Hall conductance has the same sign structure as the topological Chern number of the pure Kitaev spin liquid. This observation suggests that the non-Abelian topological order associated with fractionalization of the local magnetic moments persists even in the presence of non-Kitaev interactions in α-RuCl₃.

Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

This paper proposes natural drug candidate compounds for the treatment of coronavirus disease 2019 (COVID-19). We investigated the binding properties between the compounds in the Moringa oleifera plant and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 using molecular docking and ab initio fragment molecular orbital calculations. Among the 12 compounds, niaziminin was found to bind the strongest to Mpro. We furthermore proposed novel compounds based on niaziminin and investigated their binding properties to Mpro. The results reveal that the introduction of a hydroxyl group into niaziminin enhances its binding affinity to Mpro. These niaziminin derivatives can be promising candidate drugs for the treatment of COVID-19.

Proposal of novel potent inhibitors against androgen receptor based on ab initio molecular orbital calculations

The androgen receptor (AR), a family of nuclear receptor proteins, stimulates the transcription of androgen-responsive genes. As its abnormal activation can cause the progression of prostate cancer, numerous types of ligands for AR have been developed as promising antagonists for the treatment of prostate cancer. We previously investigated the specific interactions between AR and nine types of existing non-steroidal ligands, using molecular simulations based on molecular mechanics and ab initio fragment molecular orbital methods. The results were confirmed to be comparable to the binding affinities of these ligands observed in experiments. We here propose novel ligands as potent inhibitors against AR and investigate their binding properties to AR, using the same molecular simulations. The results indicate that the most promising ligand binds stronger to AR than the existing non-steroidal ligands, and that our proposed ligand binds strongly to a mutant-type AR, which has drug resistance to the existing non-steroidal ligands.

FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method

We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.

Hopelessness and Depression Predict Sarcopenia in Advanced CKD and Dialysis: A Multicenter Cohort Study

BACKGROUND/OBJECTIVES

Depression and hopelessness are frequently experienced in chronic kidney disease (CKD) and are generally associated with lessened physical activity. The aim of this study was to quantify the associations between sarcopenia as determined by SARC-F with both depression and hopelessness.

DESIGN AND SETTING

This multicenter cohort study involving cross-sectional and longitudinal analyses was conducted in a university hospital and four general hospitals, each with a nephrology center, in Japan.

PARTICIPANTS

Participants consisted of 314 CKD patients (mean age 67.6), some of whom were receiving dialysis (228, 73%).

MEASUREMENTS

The main exposures were depression, measured using the Center for Epidemiologic Studies Depression (CES-D) questionnaire, and hopelessness, measured using a recently developed 18-item health-related hope scale (HR-Hope). The outcomes were sarcopenia at baseline and one year after, measured using the SARC-F questionnaire. Logistic regression models were applied.

RESULTS

The cross-sectional and longitudinal analyses included 314 and 180 patients, respectively. Eighty-nine (28.3%) patients experienced sarcopenia at baseline, and 44 (24.4%) had sarcopenia at the one-year follow-up. More hopelessness (per 10-point lower, adjusted odds ratio [AOR]: 1.33, 95% confidence interval [95% CI] 1.12-1.58), depression (AOR: 1.87, 95% CI 1.003-3.49), age (per 10-year higher, AOR: 1.70, 95% CI 1.29-2.25), being female (AOR: 2.67, 95% CI 1.43-4.98), and undergoing hemodialysis (AOR, 2.92; 95% CI, 1.41-6.05) were associated with a higher likelihood of having baseline sarcopenia. More hopelessness (per 10-point lower, AOR: 1.69, 95% CI 1.14-2.51) and depression (AOR: 4.64, 95% CI: 1.33-16.2) were associated with a higher likelihood of having sarcopenia after one year.

CONCLUSIONS

Among patients with different stages of CKD, both hopelessness and depression predicted sarcopenia. Provision of antidepressant therapies or goal-oriented educational programs to alleviate depression or hopelessness can be useful options to prevent sarcopenia.

Proposal of novel inhibitors for vitamin-D receptor: Molecular docking, molecular mechanics and ab initio molecular orbital simulations

The specific binding of active vitamin-D to the vitamin-D receptor (VDR) is closely related to the onset of immunological diseases. To inhibit the binding, various compounds have been developed as potent inhibitors against VDR. Among them, a compound NS-54c, which was developed based on the first VDR antagonist TEI-9647 (25-dehydro-1α-hydroxyvitamin D₃-26,23-lactone), was revealed to posse almost 1000-fold improved antagonistic activity over the original TEI-9647. However, the reason for this significant improvement has not been elucidated. In the present study, we investigated the specific interactions between VDR and these inhibitors, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results simulated, we furthermore proposed novel inhibitors and investigated their binding properties to VDR. The results elucidate that the replacement of propyl group at the 24th site of NS-54c by a phenethyl group can enhance the binding affinity of the inhibitor to VDR. This finding provides useful information for developing novel potent inhibitors against VDR.

Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations

The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein-ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.

Protonation states of central amino acids in a zinc metalloprotease complexed with inhibitor: Molecular mechanics optimizations and ab initio molecular orbital calculations

The zinc-metalloprotease pseudolysin (PLN) secreted from bacteria degrades extracellular proteins to produce bacterial nutrition. Since PLN has a Zn ion at the inhibitor-binding site, the interactions between Zn and PLN residues as well as inhibitor can be significantly changed depending on the protonation states of PLN residues at the inhibitor-binding site. To determine stable protonation states of these residues, we here considered different protonation states for Glu and His residues located around Zn and investigated the electronic states of the PLN + inhibitor complex, using ab initio molecular simulations. The protonation state of His223 was found to significantly affect the specific interactions between PLN and the inhibitor.

Specific interactions between tau protein and curcumin derivatives: Molecular docking and ab initio molecular orbital simulations

Alzheimer's disease (AD) is the most common neurodegenerative disorder in the world, and there is currently no potent medicine for the treatment of ADs. Curcumin, a primary chemical contained in the ancient Indian herb known as turmeric, has been extensively studied and shown to be effective in inhibiting the aggregations of amyloid-β and tau proteins, both of which are observed in the brains of AD patients. In the present study, we focused on the tau protein and investigated its specific interactions with curcumin derivatives, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results, we attempted to propose novel potent inhibitors against the tau protein aggregation. Our molecular simulations provide useful information for developing novel medicines for the treatment of ADs.

TRITIUM, HYDROGEN AND OXYGEN ISOTOPE COMPOSITIONS IN MONTHLY PRECIPITATION SAMPLES COLLECTED AT TOKI, JAPAN

Monthly precipitation samples have been collected at Toki, Japan, from November 2013 to March 2017. In this report, selected data were analysed to identify the regional hydrogen and oxygen isotope compositions. Tritium (3H) concentration in the precipitation ranged from 0.10 to 0.61 Bq L-1 and higher 3H concentrations were observed in spring rather than in other seasons. This range was similar to values reported in Chiba City, Japan. 3H concentration and the ratio d-excess, and δD values were roughly clustered according to each separate season. These regional hydrogen and oxygen isotope compositions will be used for environmental assessments of effects of the deuterium plasma experiments of the large fusion test device.

P6530Clinical outcomes of dialysis patients treated with current generation DES for left main distal bifurcation

Objectives

We assessed clinical outcomes after percutaneous coronary intervention (PCI) for unprotected left main (ULM) using current generation drug eluting stents (cDES) in hemodialysis (HD) patients compared to general populations.

Methods

We identified 1269 consecutive patients who underwent PCI for ULM distal bifurcation lesions. Of them, 563 patients were treated with cDES (512 non HD and 51 HD patients). The primary endpoint was target lesion failure (TLF) at 3 years, defined as a composite of cardiac death, target lesion revascularization (TLR) and myocardial infarction (MI).

Results

HD group was more likely to have diabetes mellitus (70.0% vs. 45.8%, p=0.002), peripheral artery disease (56.0% vs. 14.9%, p<0.001), and lower ejection fraction (52.6% vs. 56.3%, p=0.026). The rate of TLF at 3 years was significantly higher in the HD group (adjusted Hazard ratio [HR] 2.59; 95% confidence interval [CI], 1.54–4.37; p<0.001). Cardiac mortality was significantly higher in the HD group (adjusted HR 4.49; 95% CI, 2.07–9.74; p<0.001). The rates of TLR for LM-left anterior descending artery (LAD) and left circumflex ostium (LCXos) were significantly higher in the HD group (LMT-LAD: adjusted HR 3.10; 95% CI, 1.31–7.33; p=0.01, LCXos: adjusted HR 2.56; 95% CI, 1.32–4.94; p=0.005). The rate of MI was similar between the 2 groups.

Conclusions

Hemodialysis was strongly associated with adverse events after PCI for ULM distal bifurcation lesions even with cDES.

Design of galardine analogs as putative psudolysin inhibitors based on ab initio fragment molecular orbital calculations

Pseudolysin (PLN) is a metalloproteinase secreted from bacteria that degrades extracellular proteins to produce bacterial nutrition. It is thus expected that inhibitors against PLN can suppress the growth of bacteria and their pandemic spread. In addition, since these inhibitors do not attack to bacteria directly, there is a reduced risk for producing drug-resistant bacteria. On the other hand, as PLN has large structural similarity in the active sites with human matrix-metalloproteinases (MMPs), there is a possibility that the inhibitors for PLN also inhibit MMP activity, resulting in a loss of necessary nutrients to be produced by MMPs. Therefore, it is required the agents inhibiting the activity of only PLN not MMPs. In the present study, we employed a hydroxamate compound galardin, which has a significant inhibition effect against PLN and MMP, and investigated its specific interactions with PLN/MMP at atomic and electronic levels, by use of ab initio molecular simulations. Based on the results, we proposed several derivatives of galardin and elucidated which derivatives that can bind more strongly to PLN and be putative antimicrobial agents capable of inhibiting the PLN activity.Communicated by Ramaswamy H. Sarma.

Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations

The transcription mechanism of genetic information from DNA to RNA is efficiently controlled by regulatory proteins, such as catabolite activator protein (CAP), and their ligands. When cyclic AMP (cAMP) binds to CAP, the complex forms a dimer and binds specifically to DNA to activate the transcription mechanism. On the other hand, when cyclic GMP (cGMP) binds to CAP, the complex has no marked effect on the mechanism. In our previous study, based on molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) methods, we elucidated which residues of CAP are important for the specific interactions between CAP and DNA in the CAP-monomer+DNA + cAMP complex. However, this monomer model for CAP cannot describe real interactions between the CAP-dimer and DNA because CAPs form a dimer before binding to DNA. Accordingly, here, we investigated stable structures and their electronic states for the CAP-dimer+DNA complex with cAMP or cGMP ligand, to clarify the influence of ligand-binding on the interactions between CAP-dimer and DNA. The MD simulations elucidated that the DNA-binding domains of CAP-dimer behave differently depending on the ligand bound to the CAP-dimer. In addition, FMO calculations revealed that the binding energy between CAP-dimer and DNA for the CAP-dimer+DNA + cAMP complex is larger than that for the CAP-dimer+DNA + cGMP complex, being consistent with experiments. It was also highlighted that the Arg185 and Lys188 residues of CAP-dimer are important for the binding between CAP-dimer and DNA. These results provide useful information for proposing new compounds that efficiently control the transcription mechanism.

Specific interactions between 2-trans enoyl-acyl carrier protein reductase and its ligand: Protein-ligand docking and ab initio fragment molecular orbital calculations

2-trans enoyl-acyl carrier protein reductase (InhA) has been identified as a promising target for the development of novel chemotherapy for tuberculosis. In the present study, a series of heteroaryl benzamide derivatives were selected as potent inhibitors against InhA, and their binding properties with InhA were investigated at atomic and electronic levels by ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics optimizations and ab initio fragment molecular orbital (FMO) calculations. The results evaluated by FMO highlight some key interactions between InhA and the derivatives, indicating that the most potent derivative has strong hydrogen bonds with the Met98 side chain of InhA and strong electrostatic interactions with the nicotinamide adenine dinucleotide cofactor. These findings provide informative structural concepts for designing novel heteroaryl benzamide derivatives with higher binding affinity to InhA.

Ligand chirality can affect histidine protonation of vitamin-D receptor: ab initio molecular orbital calculations in water

Vitamin D is recognized to play important roles in the onset of immunological diseases as well as the regulation of the amount of Ca in the blood. Since these physiological actions caused by active vitamin D are triggered by the specific interaction between the vitamin D receptor (VDR) and active vitamin D, many types of compounds have been developed as potent ligands against VDR. It was found that the binding affinity between VDR and its ligand depends significantly on the chirality of the ligand. However, the reason for the dependence has, thus far, not been elucidated. In the present study, we investigated the specific interactions between VDR and some ligands with different chirality, using ab initio fragment molecular orbital (FMO) calculations. The FMO results reveal that two histidine residues of VDR contribute significantly to the binding between VDR and ligand and that their protonation states can affect the specific interactions between VDR and ligand. We therefore considered other possible protonation states of these histidine residues and determined their most stable states, using the ab initio FMO calculations. The results illustrate the possibility that the difference in the chirality of a ligand can induce the change in protonation states of the histidine residues of VDR existing near the ligand. This finding provides an important warning that the protonation states of histidine residues existing near the ligand should be considered more precisely in the molecular simulations for investigating the specific interactions between protein and ligand.

SARC-F Validation and SARC-F+EBM Derivation in Musculoskeletal Disease: The SPSS-OK Study

OBJECTIVES

To validate the SARC-F questionnaire for sarcopenia screening in musculoskeletal disease setting, and to assess improvements in diagnostic accuracy by adding "EBM" (elderly and body mass index information) to the SARC-F.

DESIGN

Diagnostic accuracy study.

SETTING AND PARTICIPANTS

The center involved in this study was located in an urban area of Kobe City, Japan. People with musculoskeletal disease in the knee, hip, or spine who were scheduled for surgical treatment were included.

MEASUREMENTS

Sarcopenia was evaluated using the Asian Working Group for Sarcopenia (AWGS) and the European Working Group on Sarcopenia in Older People (EWGSOP2), which included bioimpedance, handgrip strength, and gait speed. Patients answered the SARC-F questionnaire and their body mass index was measured. SARC-F and "EBM" information were combined into an original score. The sensitivities, specificities, and areas under the receiver operating characteristic curve (AUC) were estimated and compared to identify sarcopenia.

RESULTS

A total of 959 patients were included. Sarcopenia by AWGS criteria was identified in 36 (3.8%) patients. SARC-F had a sensitivity of 41.7% and specificity of 68.5%. SARC-F+EBM had a sensitivity of 77.8% and specificity of 69.6%, with substantial improvement in sensitivity (P<0.001). The AUCs for SARC-F and SARC-F+EBM were 0.557 (95% confidence interval [CI] 0.452-0.662) and 0.824 (95% CI 0.762-0.886), respectively (P<0.001). Similar results were obtained when EWGSOP2 criteria were used as the reference standard.

CONCLUSION

The SARC-F alone is not adequate for finding cases in musculoskeletal disease settings. SARC-F+EBM significantly improved the sensitivity and overall diagnostic accuracy of the SARC-F for screening sarcopenia. SARC-F+EBM is potentially useful for screening sarcopenia in different ethnic and disease settings.

Unusual Thermal Hall Effect in a Kitaev Spin Liquid Candidate α-RuCl_{3}

The Kitaev quantum spin liquid displays the fractionalization of quantum spins into Majorana fermions. The emergent Majorana edge current is predicted to manifest itself in the form of a finite thermal Hall effect, a feature commonly discussed in topological superconductors. Here we report on thermal Hall conductivity κ_{xy} measurements in α-RuCl_{3}, a candidate Kitaev magnet with the two-dimensional honeycomb lattice. In a spin-liquid (Kitaev paramagnetic) state below the temperature characterized by the Kitaev interaction J_{K}/k_{B}∼80  K, positive κ_{xy} develops gradually upon cooling, demonstrating the presence of highly unusual itinerant excitations. Although the zero-temperature property is masked by the magnetic ordering at T_{N}=7  K, the sign, magnitude, and T dependence of κ_{xy}/T at intermediate temperatures follows the predicted trend of the itinerant Majorana excitations.

A novel peptide blocking cancer cell invasion by structure-based drug design

The receptor for the urokinase-type plasminogen activator (uPA), uPAR, facilitates tumor cell invasion and metastasis by focusing on several ligands, including uPA, integrins and vitronectin. With computational prediction algorithms and structure-based drug design, we identified peptides containing the Gly-Lys-Gly-Glu-Gly-Glu-Gly-Lys-Gly sequence (peptide H1), which strongly interacts with uPAR. The aim of the present study was to investigate the effect of allosteric inhibition at the uPAR interface using a novel synthetic peptide and its function on ovarian cancer cell invasion. The molecular and functional mechanisms of H1 were determined by complementary biochemical and biological methods in the promyeloid U937 cell line as well as ovarian cancer cell lines, including serous carcinoma SKOV3 and clear cell carcinoma TOV21G. The effects of H1 treatment on cancer cell invasion were evaluated in vitro. H1 inhibited cancer cell invasion, without affecting cell viability, accompanied by the suppression of extracellular signal-regulated kinase (ERK)-1 phosphorylation and then matrix metalloproteinase (MMP)-9 expression. H1 failed to block the interaction of uPA-uPAR protein-protein interaction in cells, but antagonized the uPA function. H1 failed to disrupt the uPA-uPAR complex, but abolished the invasion of ovarian cancer cells at least through suppression of the ERK-MMP-9 signaling pathway. Further studies are needed to confirm our observations and to describe the underlying molecular mechanism.

Specific interactions between vitamin-D receptor and its ligands: Ab initio molecular orbital calculations in water

Vitamin D is recognized to play important roles not only in the bone metabolism and the regulation of Ca amount in the blood but also in the onset of immunological diseases. These physiological actions caused by vitamin D are triggered by the specific interaction between vitamin D receptor (VDR) and vitamin D. In the present study, we investigated the interactions between VDR and vitamin D derivatives using ab initio molecular simulation, in order to elucidate the reason for the significant difference in their effects on VDR activity. Based on the results simulated, we elucidated which parts of the derivatives and which residues of VDR mainly contribute to the specific binding between VDR and the derivatives at an electronic level. This finding will be helpful for proposing new vitamin D derivatives as a potent modulator or inhibitor against VDR.

Specific interactions between zinc metalloproteinase and its inhibitors: Ab initio fragment molecular orbital calculations

Bacteria secrete the enzyme pseudolysin (PLN) to degrade exocellular proteins, and the produced peptides are used as a nutrient for the bacteria. It is thus expected that inhibition of PLN can suppress bacterial growth. Since such inhibitors do not attack to bacteria directly, the risk of producing drug-resistance bacteria is less. However, endogenous proteinases such as the matrix metalloproteinases (MMPs) have active site similar to that of PLN, and there is a possibility that PLN inhibitors also inhibit the activity of MMPs, resulting in a loss of substrate degradation by these proteinases. Therefore, agents that inhibit the activity of only PLN and not MMPs are required. In the present study, we select two compounds (ARP101 and LM2) and investigate their specific interactions with PLN and MMPs by use of ab initio molecular simulations. Based on the results, we propose several novel compounds as candidates for potent PLN inhibition and investigate their binding properties with PLN, elucidating that the compound, in which a toluene group is introduced into LM2, has larger binding energy with PLN compared with the pristine LM2. Therefore, this compound is suggested to be a potent PLN inhibitor.