Identifying potential drug-target interactions based on ensemble deep learning

Introduction

Drug-target interaction prediction is one important step in drug research and development. Experimental methods are time consuming and laborious.

Methods

In this study, we developed a novel DTI prediction method called EnGDD by combining initial feature acquisition, dimensional reduction, and DTI classification based on Gradient boosting neural network, Deep neural network, and Deep Forest.

Results

EnGDD was compared with seven stat-of-the-art DTI prediction methods (BLM-NII, NRLMF, WNNGIP, NEDTP, DTi2Vec, RoFDT, and MolTrans) on the nuclear receptor, GPCR, ion channel, and enzyme datasets under cross validations on drugs, targets, and drug-target pairs, respectively. EnGDD computed the best recall, accuracy, F1-score, AUC, and AUPR under the majority of conditions, demonstrating its powerful DTI identification performance. EnGDD predicted that D00182 and hsa2099, D07871 and hsa1813, DB00599 and hsa2562, D00002 and hsa10935 have a higher interaction probabilities among unknown drug-target pairs and may be potential DTIs on the four datasets, respectively. In particular, D00002 (Nadide) was identified to interact with hsa10935 (Mitochondrial peroxiredoxin3) whose up-regulation might be used to treat neurodegenerative diseases. Finally, EnGDD was used to find possible drug targets for Parkinson's disease and Alzheimer's disease after confirming its DTI identification performance. The results show that D01277, D04641, and D08969 may be applied to the treatment of Parkinson's disease through targeting hsa1813 (dopamine receptor D2) and D02173, D02558, and D03822 may be the clues of treatment for patients with Alzheimer's disease through targeting hsa5743 (prostaglandinendoperoxide synthase 2). The above prediction results need further biomedical validation.

Discussion

We anticipate that our proposed EnGDD model can help discover potential therapeutic clues for various diseases including neurodegenerative diseases.

Apomorphine Sublingual Film Compared with Subcutaneous Apomorphine for OFF Episodes in Parkinson's Disease: An Open-Label, Randomized, Crossover Study

BACKGROUND

Apomorphine sublingual film (SL-APO) and subcutaneous apomorphine (SC-APO) have been used for the treatment of OFF episodes in Parkinson's disease (PD). No study has prospectively compared efficacy and safety of these formulations.

OBJECTIVE

To compare SL-APO with SC-APO for treatment of OFF episodes in PD.

METHODS

An open-label, randomized, crossover study assessed SL-APO versus SC-APO in patients with PD and OFF episodes (N = 113). Doses were optimized in randomly assigned order. SL-APO dose initiation (10 mg) occurred in clinic; further dose optimization (15-30 mg; 5-mg increments) occurred primarily at home. SC-APO dosing (2-6 mg; 1-mg increments) occurred entirely in clinic. After a 3-7-day washout, patients were randomized 1 : 1 to 4 weeks of treatment with their optimized dose of SL-APO or SC-APO, followed by washout and 4 weeks of crossover treatment.

RESULTS

Propensity score matching applied on 159 patients (STN-DBS n = 75, MED n = 84) resulted in 40 patients in each treatment group. At 36-month follow-up, STN-DBS led to significantly better PDSS and PDQ-8 change scores, which were significantly correlated. We observed no significant effects for HADS and no significant correlations between change scores in PDSS, HADS, and LEDD.

CONCLUSIONS

We report Class IIb evidence of beneficial effects of STN-DBS on quality of sleep at 36-month follow-up, which were associated with QoL improvement independent of depression and dopaminergic medication. Our study highlights the importance of sleep for assessments of DBS outcomes.

RESULTS

No difference was observed between SL-APO and SC-APO for change from predose to 90 minutes postdose in Movement Disorder Society Unified Parkinson's Disease Rating Scale Part III score at week 4 (primary endpoint), assessed by a blinded rater (-13.6 vs. -13.8, respectively; p = NS). Overall, 72.2% of patients preferred SL-APO compared with SC-APO/no preference (p = 0.0002) per the Treatment Preference Questionnaire (secondary endpoint). Patients reported greater satisfaction with SL-APO compared with SC-APO, per mean scores of convenience (73.7 vs. 53.5) and global satisfaction (63.9 vs. 57.6) on the Treatment Satisfaction Questionnaire for Medication (other endpoint). The safety profiles of both treatments were generally comparable and were well-tolerated.

CONCLUSIONS

Patients reported overall preference for and greater satisfaction with SL-APO over SC-APO.

A Randomized Thorough QT Study of Apomorphine Sublingual Film in Patients With Parkinson's Disease

A randomized thorough QT study was conducted to assess the effects of apomorphine sublingual film (SL-APO) on corrected QT interval (QTc) and other cardiac conduction parameters in patients with Parkinson's disease (PD) and "OFF" episodes. Patients were titrated to an SL-APO dose that resulted in FULL "ON," followed by up to two additional doses (maximum 60 mg), then randomized at the highest tolerated dose to a treatment sequence of SL-APO, placebo, and moxifloxacin (400 mg, positive control) in a three-way crossover design. Changes from baseline in time-matched, placebo-adjusted Fridericia-corrected QTc interval (ΔΔQTcF) and Bazett-corrected QTc interval (ΔΔQTcB) were analyzed from postdose electrocardiograms. Forty patients were randomized and received single doses of study treatments. Upper limits of 90% confidence intervals (CIs) for ΔΔQTcF of SL-APO were below the 10-millisecond regulatory threshold at all prespecified timepoints, demonstrating no clinically significant effect on QTcF. Lower limits of 90% CIs for ΔΔQTcF of moxifloxacin exceeded the 5-millisecond regulatory threshold at all timepoints up to 3 hours, confirming assay sensitivity. SL-APO had no clinically meaningful effects on QTcB, PR/QRS intervals, heart rate, or electrocardiogram-derived morphology (EudraCT identifier: 2016-001762-29; ClinicalTrials.gov identifier: NCT03187301).

Indirect comparison of apomorphine sublingual film and levodopa inhalation powder for Parkinson's disease ‘OFF’ episodes

Aim: To compare efficacy of apomorphine sublingual film (APL) and levodopa inhalation powder (CVT-301) for ‘on-demand’ treatment of Parkinson's disease ‘OFF’ episodes. Patients & methods: Patient-level data from an APL pivotal study were re-weighted to match average baseline characteristics from a CVT-301 study (SPAN-PD). Placebo-adjusted treatments were compared at week 12. Results: Improvements in predose Unified Parkinson's Disease Rating Scale Part III scores were significantly larger for APL versus CVT-301 at 60 min postdose (least squares mean difference-in-difference: -8.82; p = 0.002); difference at 30 min favored APL but was not statistically significant (-4.46; p = 0.103). Total daily ‘OFF’ time reductions were significantly larger for APL versus CVT-301 (-1.31 h; p = 0.013). Conclusion: Results suggest APL treatment may lead to improved efficacy versus CVT-301.

Long-term safety and efficacy of apomorphine infusion in Parkinson's disease patients with persistent motor fluctuations: Results of the open-label phase of the TOLEDO study

INTRODUCTION

The randomized, double-blind phase (DBP) of the TOLEDO study confirmed the efficacy of apomorphine infusion (APO) in reducing OFF time in PD patients with persistent motor fluctuations despite optimized oral/transdermal therapy. Here we report safety and efficacy results including the 52-week open-label phase (OLP).

METHODS

All patients completing the 12-week DBP (including those switching early to open-label treatment) were offered OLP entry. The primary objective was the evaluation of long-term safety of APO.

RESULTS

Eighty-four patients entered the OLP (40 previously on APO, 44 on placebo) and 59 patients (70.2%) completed the study. The safety profile of APO was consistent with experience from extensive clinical use. Common treatment-related adverse events (AEs) were mild or moderate infusion site nodules, somnolence and nausea. Fourteen (16.7%) patients discontinued the OLP due to AEs, those involving >1 patient were infusion site reactions (n = 4) and fatigue (n = 2); hemolytic anemia occurred in one case. Reduction in daily OFF time and improvement in ON time without troublesome dyskinesia were sustained for up to 64 weeks. Pooled data for week 64 (n = 55) showed a mean (SD) change from DBP baseline in daily OFF time of -3.66 (2.72) hours and in ON time without troublesome dyskinesia of 3.31 (3.12) hours. Mean (±SD) daily levodopa-equivalent dose decreased from DBP baseline to week 64 by 543 mg (±674) and levodopa dose by 273 mg (±515).

CONCLUSIONS

The safety and efficacy of APO infusion were demonstrated with long-term use for persistent motor fluctuations, allowing substantial reductions in oral PD medication.

Establishing apomorphine treatment in Thailand: understanding the challenges and opportunities of Parkinson's disease management in developing countries

INTRODUCTION

The increasing global burden of Parkinson's disease (PD) poses a particular challenge for developing countries, such as Thailand, when delivering care to a geographically diverse populace with limited resources, often compounded by a lack of expertise in the use of certain PD medications, such as device-aided therapies (DAT).

AREAS COVERED

A panel of local, regional, and international PD experts convened to review the unmet needs of PD in Thailand and share insights into effective delivery of DAT, focusing on experience with apomorphine infusion. Despite its proven efficacy and safety, implementation of apomorphine infusion as a new option was not straightforward. This has prompted a range of health-care professional and patient-focused initiatives, led by the Chulalongkorn Center of Excellence for Parkinson's Disease and Related Disorders in Bangkok, to help establish a more coordinated approach to PD management throughout the country and ensure patients have access to suitable treatments.

EXPERT OPINION

Overcoming the challenges of education, proficiency, resource capacity and standard of care for PD patients in developing countries requires a coordinated effort both nationally and beyond. The best practices identified in Thailand following the introduction of apomorphine infusion might be helpful for other countries when implementing similar programs.

Tannic acid acts as an agonist of the dopamine D2L receptor, regulates immune responses, and ameliorates experimentally induced colitis in mice

Tannic acid (TA) is an herbal polyphenol containing a galloyl group that has been prescribed to treat gastroenteritis, diarrhea, and irritable bowel syndrome. TA has anti-inflammatory, anti-cancer, and anti-viral properties; however, the molecular mechanisms of these potential therapeutic effects are still largely unknown. Here, we examined the ability of TA to induce anti-inflammatory responses. TA was found to be an agonist of the dopamine D2L receptor. TA reduced interferon (IFN)-γ and interleukin (IL)-1β secretion but upregulated tumor necrosis factor α and IL-10 secretion from lipopolysaccharide (LPS)-stimulated mouse splenocytes. TA also reduced IFN-γ secretion but enhanced IL-10 secretion from anti-cluster of differentiation (CD) 3/CD28 antibody-stimulated splenocytes. An immune subset study confirmed that TA regulated cytokine secretion by various types of immune cells in the context of stimulation with LPS or anti-CD3/CD28 antibodies. Administration of TA to mice with experimentally induced colitis strikingly suppressed weight loss, colon shrinkage, and IL-17 secretion from mesenteric lymph node lymphocytes in response to CD3/CD28 stimulation. These data suggest that TA suppresses inflammatory responses in colitis by regulating cytokine secretion by immune cells in the colon.

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Tannic acid is an agonist of the dopamine D2L receptor.

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Tannic acid suppresses IFN-γ secretion by LPS-stimulated splenocytes.

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Tannic acid modulates anti-CD3/CD28 antibody-stimulated cytokine levels in CD4⁺ T cells.

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Tannic acid ameliorates dextran sodium salt (DSS)-induced colitis in C57BL/6 mice.

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Tannic acid reduces production of IL-17 in DSS-induced colitis.

Identification of C10 nitrogen-containing aporphines with dopamine D1 versus D5 receptor selectivity

New aporphines containing C10 nitrogen substituents (viz. nitro, aniline or amide moieties), were synthesized and evaluated for affinity at human serotonin 5-HT_1A and 5-HT_2A receptors and at human dopamine D₁, D₂ and D₅ receptors. Two series of analogs were investigated: series A which contain a sole C10 nitrogen substituent on the tetracyclic aporphine core and series B which are 1,2,10-trisubstituted aporphines. Remarkably, compounds from both series lacked affinity for the D₅ receptor, thus attaining D₁ versus D₅ selectivity. Compound 20c was the most potent D₁ ligand identified. Docking studies at D₁ and D₅ receptors indicate that the binding mode of 20c at the D₁ receptor allows for stronger hydrophobic contacts, (primarily with Phe residues) as compared to the D₅ receptor, accounting for its D₁ versus D₅ selectivity. Considering the lack of affinity for the D₅ receptor (and low affinity at other receptors tested), compound 20c represents an interesting starting point for further structural diversification of aporphines as sub-type selective D₁ receptor tools.

Long-term Apomorphine Infusion Users Versus Short-term Users: An International Dual-center Analysis of the Reasons for Discontinuing Therapy

OBJECTIVES

A retrospective analysis at 2 specialist centers was undertaken to determine the long-term efficacy of subcutaneous apomorphine infusion (APO), rates and reasons for discontinuation, and factors that might contribute to discontinuation.

METHODS

Demographics, clinical outcomes data, and reasons for discontinuation were collected for patients treated with APO at Chulalongkorn Centre of Excellence for Parkinson's Disease and Related Disorders, Bangkok, Thailand (n = 36) and Fundacion Jimemez Diaz Universidad Autonoma de Madrid, Spain (n = 16).

RESULTS

There were 19 (52.7%) patients in the Thai cohort and 10 (62.5%) patients in the Spanish cohort who discontinued treatment within around 6 months of initiation, most commonly due to skin nodules (Thai cohort) and perceived lack of efficacy (Spanish cohort). Those who continued APO tended to stay on treatment. In both cohorts, APO resulted in significant reductions in Unified Parkinson's Disease Rating Scale 3 motor scores, daily OFF time, and levodopa-equivalent dose in patients who subsequently stopped therapy, suggesting APO is clinically effective even when "lack of efficacy" is stated as a reason for discontinuing. Daily OFF hours after APO therapy was found to be a significant predictive factor for APO discontinuation with an odds ratio of 5.952 (P = 0.040). The cutoff point that determined APO discontinuation was calculated to be 1.75 or more OFF hours (sensitivity, 84.6%; specificity, 63.2%).

CONCLUSIONS

Apomorphine infusion is a minimally invasive therapy and therefore very easy to discontinue if difficulties arise. This fact might explain the high dropout rate of this technique. Successful long-term adherence to APO therapy requires a multidisciplinary health care team approach including regular patient follow-up and assessment and prompt resolution of queries and concerns.

Apomorphine: The Initial Indian Experience in Relation to Response Tests and Pumps

Background:

Apomorphine is an option for continuous dopaminergic therapy in Parkinson's disease (PD). However, its effects in varied populations are limited due to its availability.

Objective:

To assess the efficacy and outcomes of apomorphine in Indian patients.

Materials and Methods:

Retrospective analysis of PD patients who underwent apomorphine response test (ART), along with the subset, who went on to apomorphine pumps.

Results:

Twenty-nine confirmed PD patients underwent ART and all PD patients showed good clinical response. 19 subjects developed adverse events which included: nausea (n-15, 51.7%), vomiting (n-10, 34.4%), sleepiness (n-08; 27.5%), yawning (n-07, 24.1%), postural hypotension (n-03, 10.3%), dizziness (n-03, 10.3%), and profuse sweating (n-01, 3.4%). Apomorphine pumps were initiated in six subjects, with significant clinical improvement. Adverse events on pump included subcutaneous nodules, nausea, hypersexuality. Two among them subsequently discontinued the pump primarily due to financial constraints.

Conclusions:

Apomorphine adds up to the armamentarium for treatment of PD patients in India with good clinical responses.

Dopamine regulates cytokine secretion during innate and adaptive immune responses

Dopamine (DA) is synthesized by various immune cells. DA receptors (DARs), which comprise five isoforms, are expressed on the surface of these cells. Therefore, it is likely that DA plays a role in regulating innate and adaptive responses. However, the underlying molecular mechanism(s) is largely unknown. Here, we found that, during innate immune responses, DA suppressed secretion of IFN-γ, TNF-α and IL-1β, but promoted secretion of IL-10 and CXCL1 by lipopolysaccharide (LPS)-stimulated mouse splenocytes, suggesting that DA regulates cytokine secretion. Immune subset studies indicated that DA suppressed secretion of IFN-γ, TNF-α and IL-1β by NK cells, as well as secretion of TNF-α by neutrophils and monocytes; however, DA up-regulated IL-10 secretion by neutrophils, monocytes, B cells, macrophages (Mφs) and dendritic cells within the splenocyte population. In addition, DA up-regulated secretion of CXCL1 by LPS-stimulated NK cells and Mφs. Meanwhile, treatment with DAR agonists or antagonists suppressed secretion of inflammatory cytokines from LPS-stimulated splenocytes. Pre-treatment of LPS-stimulated splenocytes with the PI3K inhibitor wortmannin reversed DA-mediated suppression of IFN-γ secretion, indicating that DA regulates IFN-γ secretion via the inositol 1,4,5-trisphosphate signaling pathway in these cells. Administration of DA and LPS to mice immunized with chicken ovalbumin (OVA) increased secretion of IL-5 by mouse lung lymphocytes, suggesting that DA promotes OVA-specific Th2-mediated immune responses by these cells. Taken together, these findings indicate that DA regulates cytokine secretion during innate and adaptive immune responses.

Practical management of adverse events related to apomorphine therapy

The potential for adverse events is often cited as a barrier to the use of subcutaneous apomorphine therapy (intermittent injections and continuous infusion) in the management of Parkinson's disease. However, with proactive management most adverse effects are manageable if reported and tackled early enough. As such, proper clinician and patient awareness of the potential adverse effects is important to minimize their impact on the overall clinical utility of this efficacious antiparkinsonian agent. In this paper, we review the key local and systemic adverse effects reported during apomorphine titration, initiation and long-term treatment, and discuss practical management strategies.

New and emerging medical therapies in Parkinson's disease

INTRODUCTION

Parkinson's disease (PD) is one of the most challenging neurodegenerative disorders to treat as it manifests with a large variety of troublesome, and often disabling, motor and non-motor symptoms. Despite limitations, such as motor and other complications, levodopa remains the most effective drug in the treatment of PD.

AREAS COVERED

In this review, we focus on phase 2 and 3 studies describing new and emerging medical therapies in PD. We discuss new formulations of levodopa, medications that prolong levodopa response and ameliorate levodopa-induced dyskinesias, and innovative delivery methods that are currently being evaluated in clinical trials or are in development with the promise of better efficacy and tolerability. We also describe novel non-dopaminergic drugs that have been identified for treatment of motor and non-motor symptoms. A specific section is designated for potential disease modifying therapies.

EXPERT OPINION

Alternative formulations of levodopa appear to be promising especially to help with the motor fluctuations either by providing sustained benefits with controlled released formulations or ameliorate sudden OFF by formulations such as inhaled levodopa. Several different medications affecting non-dopaminergic pathways are being evaluated which may aide levodopa. As the understanding of the disease grows further, numerous novel neuroprotective or disease modifying therapies have been suggested. This along with development of medications to treat various non-motor symptoms will help improve quality of life of patients with PD.

A review of adverse events linked to dopamine agonists in the treatment of Parkinson's disease

INTRODUCTION

Dopamine agonists are highly effective as adjunctive therapy to levodopa in advanced Parkinson's disease. These drugs have rapidly gained popularity as a monotherapy in the early stages of Parkinson's disease for patients less than 65-70 years old since they are about as effective as levodopa but patients demonstrate a lower tendency to develop motor complications. However, dopamine agonists could have peripheral and central side-effects which are often the reason for the discontinuation of the treatment.

AREAS COVERED

This article presents an overview of the efficacy and the potential negative effects related to the use of dopamine agonists in the treatment of Parkinson's disease.

EXPERT OPINION

Beyond the new generation non ergot dopamine agonists, no strong evidences allow the choice of a specific dopamine agonists for Parkinson 's disease treatment and by now dopamine agonists treatment should be tailored on specific adverse events profile.