Applying deep learning to iterative screening of medium-sized molecules for protein-protein interaction-targeted drug discovery

We combined a library of medium-sized molecules with iterative screening using multiple machine learning algorithms that were ligand-based, which resulted in a large increase of the hit rate against a protein-protein interaction target. This was demonstrated by inhibition assays using a PPI target, Kelch-like ECH-associated protein 1/nuclear factor erythroid 2-related factor 2 (Keap1/Nrf2), and a deep neural network model based on the first-round assay data showed a highest hit rate of 27.3%. Using the models, we identified novel active and non-flat compounds far from public datasets, expanding the chemical space.

DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions

Protein-protein interactions (PPIs) are recognized as important targets in drug discovery. The characteristics of molecules that inhibit PPIs differ from those of small-molecule compounds. We developed a novel chemical library database system (DLiP) to design PPI inhibitors. A total of 32,647 PPI-related compounds are registered in the DLiP. It contains 15,214 newly synthesized compounds, with molecular weight ranging from 450 to 650, and 17,433 active and inactive compounds registered by extracting and integrating known compound data related to 105 PPI targets from public databases and published literature. Our analysis revealed that the compounds in this database contain unique chemical structures and have physicochemical properties suitable for binding to the protein-protein interface. In addition, advanced functions have been integrated with the web interface, which allows users to search for potential PPI inhibitor compounds based on types of protein-protein interfaces, filter results by drug-likeness indicators important for PPI targeting such as rule-of-4, and display known active and inactive compounds for each PPI target. The DLiP aids the search for new candidate molecules for PPI drug discovery and is available online (https://skb-insilico.com/dlip).

The efficacy of general anesthesia during pulmonary vein isolation compared with conscious sedation

Background

Catheter ablation (RFA) is significantly more effective in terms of arrhythmia recurrence rate than antiarrhythmic medication. For the duration of the procedure, the patient needs to remain motionless on the operation table. General anesthesia (GA) is widely used during atrial fibrillation (AF) ablation in all over the world, however RFA of AF is performed under conscious sedation (CS) in the most centers in Japan.

It remains controversial whether cardiac anesthesiologists are best suited to manage anesthesia in the electrophysiology lab.

Objective

The aim of this study was to report the efficacy and safety of GA during AF ablation.

Methods

297 patients (67.3±11.7 years, 208 men, 128 paroxysmal, mean follow up 443 days±306) with AF undergoing RFA in our department from January 2018 to December 2021 were retrospectively analyzed. 113 assigned to the GA group, 184 patients to the CS group.

The primary efficacy end point was radiofrequency time, ablation index, force time integral. The secondary end points defined AF recurrence and the complications.

Result

There was no difference in the baseline characteristics between the two groups. There was no difference between groups in AF recurrence (22.1% vs. 14.1%, P=0.103) and complications.However, Patients in GA had shorter radiofrequency times (66.9±3.7 minute vs 79.0±2.9 minutes P=0.01)Ablation index (376±18.6 vs 371±22.6 P<0.05), Force time integral (136±22.3 vs 111.4±45.3).

Conclusion

General anesthesia is superior to conscious sedation with shorter radiofrequency times and higher than Force time integral, ablation index. Moreover, it is not inferior in regard to arrhythmia recurrence or complication rates of catheter ablation of atrial fibrillation.

Funding Acknowledgement

Type of funding sources: None.

Safety and efficacy of a hyperaemic agent, intracoronary nicorandil 4mg, for invasive physiological assessments during fractional flow reserve measurement

Background

Fractional flow reserve (FFR) is one of most reliable index for the determining the functional severity coronary artery stenosis. Adenosine is the most commonly used agent for maximal hyperaemia. However, adenosine can cause chest discomfort, bronchial hyper-reactivity, and atrioventricular block. The aim of this study is to evaluate the safety and efficacy of intracoronary nicorandil as an alternative hyperaemic agent for FFR.

Methods and results

We enrolled consecutive 82 patients (87 lesions) who underwent FFR measurement in our center from Nov. 2018. We compared three groups; intravenous infusion of adenosine (150 μg/kg/min); and adenosine added intracoronary nicorandil 2mg; and intracoronary nicorandil 4mg. Mean FFR value was 0.83±0.09, 0.82±0.09, 0.82±0.08, There was a strong correlation among three groups (R2>0.9). Mean cyclic change in FFR was 0.026±0.023, 0.019±0.010, 0.016±0.014, respectively, cyclic change was smallest in intracoronary nicorandil 4mg group (vs ATP; p<0.001, vs ATP + nicorandil 2mg; p<0.001). By Wilcoxon test, mean FFR value of nicorandil 4mg was significant lower than ATP (p=0.0021), and equal to ATP + nicorandil 2mg (p=0.98).

Conclusions

Intracoronary nicorandil 4mg is a simple, safe, and effective way to induce steady-state hyperaemia for FFR.

Figure 1

Funding Acknowledgement

Type of funding source: None

Distribution of gene segments of the pandemic A(H1N1) 2009 virus lineage in pig populations

Swine influenza viruses (SIVs) are important not only for pig farming, but also for public health. In fact, pandemic A(H1N1) 2009 viruses [A(H1N1)pdm09] were derived from SIVs. Therefore, timely characterization of locally circulating SIVs is necessary for understanding the global status of SIVs. To genetically characterize SIVs circulating in Japanese pig populations, we isolated 24 SIVs of three subtypes (17 H1N1, four H1N2 and three H3N2 strains) from 14 pig farms in Japan from 2013 to 2016. Genetic analyses revealed that the haemagglutinin (HA) and neuraminidase (NA) genes of the 17 H1N1 and the HA gene of one H1N2, A/swine/Aichi/02/2016 (H1N2), SIVs belonged to the A(H1N1)pdm09 lineage. More importantly, all of the remaining six gene segments (i.e., PB1, PB1, PA, NP, M and NS) of the 24 SIVs, regardless of the HA and NA subtype, were also classified as belonging to the A(H1N1)pdm09 lineage. These results indicate that gene segments of A(H1N1)pdm09 lineage are widely distributed in SIVs circulating in Japanese pig populations In addition, the NA gene of A/swine/Aichi/02/2016 (H1N2) shared less than 88.5% nucleotide identity with that of the closest relative A/swine/Miyagi/5/2003 (H1N2), which was isolated in Japan in 2003. These results indicate the sustained circulation of classical H1N2-derived SIVs with remarkable diversity in the NA genes in Japanese pig populations. These findings highlight the necessity of both intensive biosecurity systems and active SIV surveillance in pig populations worldwide for both animal and public health.

A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase

¹⁹F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose. Herein a combination of ¹⁹F NMR and SPR was used to find novel binders to the ATP-binding pocket of MAP kinase extracellular regulated kinase 2 (ERK2) by fragment screening with an original fluorinated-fragment library. The ¹⁹F NMR screening yielded a high primary hit rate of binders to the ERK2 ATP-binding pocket compared with the rate for the SPR screening. Hit compounds were evaluated and categorized according to their ability to bind to different binding sites in the ATP-binding pocket. The binding manner was characterized by using isothermal titration calorimetry and docking simulation. Combining ¹⁹F NMR with other biophysical methods allows the identification of multiple types of hit compounds, thereby increasing opportunities for drug design using preferred fragments.

Activation of c-Jun N-terminal kinase by Akabane virus is required for apoptosis

Akabane virus (AKAV) belongs to the Simbu serogroup of the genus Orthobunyavirus in the family Bunyaviridae. It has been shown that AKAV induces apoptosis in mammalian cells. It is necessary to understand the signaling pathways involved in AKAV-induced apoptosis to further elucidate the molecular virology of AKAV. c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK) are mediators of apoptosis; therefore, we investigated the roles of JNK and p38 MAPK cascades in AKAV-infected cells. We found that JNK and p38 MAPK as well as their downstream substrates, c-Jun and heat shock protein 27 (HSP27), were phosphorylated in response to AKAV infection. A JNK inhibitor (SP600125) inhibited AKAV-mediated apoptosis whereas a p38 MAPK inhibitor (SB203580) did not. We conclude that AKAV infection activates the JNK and p38 MAPK signaling pathways, and the JNK cascade plays a crucial role in AKAV-induced apoptosis in vitro.

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JNK and p38 MAPK were phosphorylated in response to Akabane virus infection.

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Downstream substrates, c-Jun and heat shock protein 27, were also phosphorylated by viral infection.

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JNK inhibitor (SP600125) inhibited AKAV-mediated apoptosis whereas a p38 MAPK inhibitor (SB203580) did not.

Generation of a sensitive TNFR2-specific murine assays system

Tumor necrosis factor (TNF)/TNF receptors (TNFR1/TNFR2) are considered to be potential drug targets to treat refractory diseases, including autoimmune diseases and malignant tumors. However, their specific functions, especially in the case of TNFR2, are poorly understood. In this study, we constructed a mouse TNFR2 (mTNFR2)-mediated biological assay system that shows no effects of mouse TNFR1 (mTNFR1) in order to screen mTNFR2-selective stimulating agents. Mouse TNFR1(-/-)R2(-/-) preadipocytes were transfected with the gene encoding the mTNFR2/mouse Fas (mFas) chimeric receptor in which the extracellular and transmembrane domains of mTNFR2 were fused to the intracellular domain of mFas. Our results demonstrated that this cell line exhibits highly sensitive mTNFR2-mediated cytotoxic effects. We propose that this mTNFR2-mediated biological assay system would be a useful tool to screen for mTNFR2-selective stimulating agents.

Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice

Excessive angiogenesis contributes to numerous diseases, including cancer and blinding retinopathy. Antibodies against vascular endothelial growth factor (VEGF) have been approved and are widely used in clinical treatment. Our previous studies using SRPIN340, a small molecule inhibitor of SRPK1 (serine-arginine protein kinase 1), demonstrated that SRPK1 is a potential target for the development of antiangiogenic drugs. In this study, we solved the structure of SRPK1 bound to SRPIN340 by X-ray crystallography. Using pharmacophore docking models followed by in vitro kinase assays, we screened a large-scale chemical library, and thus identified a new inhibitor of SRPK1. This inhibitor, SRPIN803, prevented VEGF production more effectively than SRPIN340 owing to the dual inhibition of SRPK1 and CK2 (casein kinase 2). In a mouse model of age-related macular degeneration, topical administration of eye ointment containing SRPIN803 significantly inhibited choroidal neovascularization, suggesting a clinical potential of SRPIN803 as a topical ointment for ocular neovascularization. Thus SRPIN803 merits further investigation as a novel inhibitor of VEGF.

Ten-year incidences of self-reported non-vertebral fractures in Japanese patients with rheumatoid arthritis: discrepancy between disease activity control and the incidence of non-vertebral fracture

Despite improvements in rheumatoid arthritis disease activity of in the past 10 years, the incidence of self-reported non-vertebral fractures did not decrease in our cohort of 9,987 patients. This study may indicate that osteoporosis treatment and non-vertebral fracture prevention remain important regardless of the rheumatoid arthritis disease activity.

INTRODUCTION

Although rheumatoid arthritis (RA) is a risk factor for osteoporosis and fractures, few studies have described the association between disease activity and the fracture incidence in patients with RA. This study aimed to investigate changes in the non-vertebral fracture incidence between 2001 and 2010 in our Institute of Rheumatology Rheumatoid Arthritis (IORRA) cohort.

METHODS

The IORRA is a prospective observational cohort study of Japanese RA patients. A total of 9,987 patients with RA were enrolled in this cohort from 2000 to 2010. The clinical parameter and non-vertebral fracture occurrence data were collected biannually through self-reported questionnaires. Incidences of self-reported non-vertebral fractures were also analyzed via standardization according to gender, age, and disease activity during each 2-year period.

RESULTS

From 2001 to 2010, the percentage of patients with 28-joint disease activity score remission increased from 7.8 to 39.7%, prednisolone intake decreased from 51.4 to 41.3%, and bisphosphonate intake increased from 5.0 to 23.4%. The non-vertebral fracture incidence rates were 24.6/1,000 person-years in 2001 and 35.5/1,000 person-years in 2010, with no apparent change even after standardization. The overall non-vertebral fracture incidence was significantly higher in the autumn/winter than in the spring/summer (p = 0.02).

CONCLUSION

Despite improvements in disease activity and functional disability, the non-vertebral fracture incidence exhibited no apparent change between 2001 and 2010 in our patients with RA. Osteoporosis treatment and non-vertebral fracture prevention remain important regardless of the disease control in patients with RA.

Antidiabetic sulfonylureas and cAMP cooperatively activate Epac2A

Sulfonylureas are widely used drugs for treating insulin deficiency in patients with type 2 diabetes. Sulfonylureas bind to the regulatory subunit of the pancreatic β cell potassium channel that controls insulin secretion. Sulfonylureas also bind to and activate Epac2A, a member of the Epac family of cyclic adenosine monophosphate (cAMP)-binding proteins that promote insulin secretion through activation of the Ras-like guanosine triphosphatase Rap1. Using molecular docking simulation, we identified amino acid residues in one of two cyclic nucleotide-binding domains, cNBD-A, in Epac2A predicted to mediate the interaction with sulfonylureas. We confirmed the importance of the identified residues by site-directed mutagenesis and analysis of the response of the mutants to sulfonylureas using two assays: changes in fluorescence resonance energy transfer (FRET) of an Epac2A-FRET biosensor and direct sulfonylurea-binding experiments. These residues were also required for the sulfonylurea-dependent Rap1 activation by Epac2A. Binding of sulfonylureas to Epac2A depended on the concentration of cAMP and the structures of the drugs. Sulfonylureas and cAMP cooperatively activated Epac2A through binding to cNBD-A and cNBD-B, respectively. Our data suggest that sulfonylureas stabilize Epac2A in its open, active state and provide insight for the development of drugs that target Epac2A.

Optimized method of G-protein-coupled receptor homology modeling: its application to the discovery of novel CXCR7 ligands

Homology modeling of G-protein-coupled seven-transmembrane receptors (GPCRs) remains a challenge despite the increasing number of released GPCR crystal structures. This challenge can be attributed to the low sequence identity and structural diversity of the ligand-binding pocket of GPCRs. We have developed an optimized GPCR structure modeling method based on multiple GPCR crystal structures. This method was designed to be applicable to distantly related receptors of known structural templates. CXC chemokine receptor (CXCR7) is a potential drug target for cancer chemotherapy. Homology modeling, docking, and virtual screening for CXCR7 were carried out using our method. The predicted docking poses of the known antagonists were different from the crystal structure of human CXCR4 with the small-molecule antagonist IT1t. Furthermore, 21 novel CXCR7 ligands with IC50 values of 1.29-11.4 μM with various scaffolds were identified by structure-based virtual screening.

Prediction of contralateral inguinal hernias in children: a prospective study of 357 unilateral inguinal hernias

Purpose

Previously, we established a pre-operative risk scoring system to predict contralateral inguinal hernia in children with unilateral inguinal hernias. The current study aimed to verify the usefulness of our pre-operative scoring system.

Methods

This was a prospective study of patients undergoing unilateral inguinal hernia repair from 2006 to 2009 at a single institution. Gender, age at initial operation, birth weight, initial operation side, and the pre-operative risk score were recorded. We analyzed the incidence of contralateral inguinal hernia, risk factors, and the usefulness of our pre-operative risk scoring system. The follow-up period was 36 months. We used forward multiple logistic regression analysis to predict contralateral hernia.

Results

Of the 372 patients who underwent unilateral hernia repair, 357 (96.0 %) were completely followed-up for 36 months, and 23 patients (6.4 %) developed a contralateral hernia. Left-sided hernia (OR = 5.5, 95 %, CI = 1.3–24.3, p = 0.023) was associated with an increased risk of contralateral hernia. The following covariates were not associated with contralateral hernia development: gender (p = 0.702), age (p = 0.215), and birth weight (p = 0.301). The pre-operative risk score (cut-off point = 4.5) of the patients with a contralateral hernia was significantly higher, compared with the patients without a contralateral hernia using the area under the receiver operating characteristic curve (p = 0.024).

Conclusions

Using multivariate analysis, we confirmed usefulness of our pre-operative scoring system and initial side of the inguinal hernia, together, for the prediction of contralateral inguinal hernia in children.

Risk factors associated with the occurrence of hip fracture in Japanese patients with rheumatoid arthritis: a prospective observational cohort study

Risk factors associated with the occurrence of hip fracture in Japanese patients with rheumatoid arthritis (RA) were evaluated in a prospective, observational cohort study. Physical disability, advanced age, history of total knee replacement (TKR), and low body mass index (BMI) appear to be associated with the occurrence of hip fracture.

INTRODUCTION

This study seeks to evaluate the association between potential risk factors and the occurrence of hip fractures in Japanese RA patients.

METHODS

A total of 9,720 patients (82.1% female; mean age, 55.7 years) with RA were enrolled in a prospective observational study from 2000 to 2010. Self-reported hip fractures were verified using patient medical records. Cox proportional hazards models were used to analyze independent contributions of various risk factors to hip fracture occurrence.

RESULTS

During a mean follow-up of 5.2 years, 152 patients reported 152 hip fractures. Among these patients, 97 hip fractures in 97 patients (15 males, 82 females) were verified with medical records. Japanese version of the Health Assessment Questionnaire (J-HAQ) disability score [per 1 score, hazard ratio (HR), 2.64; 95% confidence interval (CI), 1.94-3.58], age (per 10 years; HR, 1.53; 95% CI, 1.25-1.87), history of TKR (HR, 3.75; 95% CI, 1.57-8.96), and BMI (per 1 kg/m2, HR, 0.92; 95% CI, 0.86-0.99) were significantly associated with hip fractures. Among the scores on the eight domains of the J-HAQ, J-HAQ (arising) (HR, 1.74; 95% CI, 1.28-2.36) and J-HAQ (hygiene) (HR, 1.58; 95% CI, 1.11-2.24) were significantly correlated with the occurrence of hip fracture.

CONCLUSIONS

High J-HAQ disability score, advanced age, history of TKR, and low BMI appear to be associated with the occurrence of hip fractures in Japanese RA patients. Among the eight domains of the J-HAQ, arising and hygiene disabilities appear to be correlated with the occurrence of hip fractures in this patient population.

Spontaneous migration of a redundant nerve root accompanied by absorption of lumbar disk herniation. A case report

A redundant nerve root is defined as a large, elongated and tortuous nerve root commonly associated with severe lumbar spinal canal stenosis. Elongation of nerve roots as a result of mechanical trapping at stenotic level is assumed to be a possible mechanism. Here we present a case in a patient who showed a redundant nerve root above the level of a lumbar canal stenosis caused by disk herniation and redundancy spontaneously migrating to a lower lumbar stenosis level accompanied by absorption of the herniated disk as shown by magnetic resonance imaging (MRI). A 67-year-old Japanese woman presented with bilateral thigh/leg pain and intermittent claudication. A midsagittal T2-weighted MR image of the lumbar spine revealed severe spinal canal stenosis at the L3-4 and L4-5 levels. At the L3-4 level, central disk herniation compressed the dural tube. An MR image revealed redundant nerve roots just cranial to the severely compressed L3-4 level. A follow-up MRI study revealed regression of disk herniation at the L3-4 level. In contrast, there was no significant change of the stenosis at the L4-5 level. Sagittal T2-weighted MR imaging at follow-up revealed redundant nerve roots just cranial to the L4-5 level, whereas the redundant nerve roots cranial to the L3-4 level had disappeared. The MRI findings of the present case support the "squeeze" hypothesis as causative of redundant nerve roots.

Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions

Druggable Protein–protein Interaction Assessment System (Dr. PIAS) is a database of druggable protein–protein interactions (PPIs) predicted by our support vector machine (SVM)-based method. Since the first publication of this database, Dr. PIAS has been updated to version 2.0. PPI data have been increased considerably, from 71 500 to 83 324 entries. As the new positive instances in our method, 4 PPIs and 10 tertiary structures have been added. This addition increases the prediction accuracy of our SVM classifier in comparison with the previous classifier, despite the number of added PPIs and structures is small. We have introduced the novel concept of ‘similar positives’ of druggable PPIs, which will help researchers discover small compounds that can inhibit predicted druggable PPIs. Dr. PIAS will aid the effective search for druggable PPIs from a mine of interactome data being rapidly accumulated. Dr. PIAS 2.0 is available at http://www.drpias.net.

Database URL: http://www.drpias.net.