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Tayebi J, BabaAli B. EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing. J Chem Inf Model 2024; 64:1868-1881. [PMID: 38483449 DOI: 10.1021/acs.jcim.3c01925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The lengthy and expensive process of developing new drugs from scratch, coupled with a high failure rate, has prompted the emergence of drug repurposing/repositioning as a more efficient and cost-effective approach. This approach involves identifying new therapeutic applications for existing approved drugs, leveraging the extensive drug-related data already gathered. However, the diversity and heterogeneity of data, along with the limited availability of known drug-disease interactions, pose significant challenges to computational drug design. To address these challenges, this study introduces EKGDR, an end-to-end knowledge graph-based approach for computational drug repurposing. EKGDR utilizes the power of a drug knowledge graph, a comprehensive repository of drug-related information that encompasses known drug interactions and various categorization information, as well as structural molecular descriptors of drugs. EKGDR employs graph neural networks, a cutting-edge graph representation learning technique, to embed the drug knowledge graph (nodes and relations) in an end-to-end manner. By doing so, EKGDR can effectively learn the underlying causes (intents) behind drug-disease interactions and recursively aggregate and combine relational messages between nodes along different multihop neighborhood paths (relational paths). This process generates representations of disease and drug nodes, enabling EKGDR to predict the interaction probability for each drug-disease pair in an end-to-end manner. The obtained results demonstrate that EKGDR outperforms previous models in all three evaluation metrics: area under the receiver operating characteristic curve (AUROC = 0.9475), area under the precision-recall curve (AUPRC = 0.9490), and recall at the top-200 recommendations (Recall@200 = 0.8315). To further validate EKGDR's effectiveness, we evaluated the top-20 candidate drugs suggested for each of Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Javad Tayebi
- School of Mathematics, Statistics and Computer Science, University of Tehran, Tehran 141556455, Iran
| | - Bagher BabaAli
- School of Mathematics, Statistics and Computer Science, University of Tehran, Tehran 141556455, Iran
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Siddique YH, Rahul, Idrisi M, Shahid M. Effect of Cabergoline on Cognitive Impairments in Transgenic Drosophila Model of Parkinson’s Disease. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200514100917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Parkinson’s disease is a common neurodegenerative disorder characterized
by selective loss of dopaminergic neurons in the substantia nigra pars compacta.
Introduction:
The effects of alpha synuclein, parkin mutation and pharmacological agents have
been studied in the Drosophila model.
Methods:
The effect of cabergoline was studied on the cognitive impairments exhibited by the
transgenic Drosophila expressing human alpha-synuclein in the neurons. The PD flies were allowed
to feed on the diet having 0.5, 1 and 1.5 μM of cabergoline.
Results and Discussion:
The exposure of cabergoline not only showed a dose-dependent significant
delay in the cognitive impairments but also prevented the loss of dopaminergic neurons. Molecular
docking studies showed the positive interaction between cabergoline and alpha-synuclein.
Conclusion:
The results suggest a protective effect of cabergoline against the cognitive impairments.
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Affiliation(s)
- Yasir Hasan Siddique
- Drosophila Transgenic Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Rahul
- Drosophila Transgenic Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Mantasha Idrisi
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd. Shahid
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
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Khanam S, Naz F, Ali F, Smita Jyoti R, Fatima A, Khan W, Singh BR, Naqvi AH, Siddique YH. Effect of cabergoline alginate nanocomposite on the transgenic Drosophila melanogaster model of Parkinson’s disease. Toxicol Mech Methods 2018; 28:699-708. [DOI: 10.1080/15376516.2018.1502386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Saba Khanam
- Department of Zoology, Section of Genetics, Drosophila Transgenic Laboratory, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Falaq Naz
- Department of Zoology, Section of Genetics, Drosophila Transgenic Laboratory, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Fahad Ali
- Department of Zoology, Section of Genetics, Drosophila Transgenic Laboratory, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Rahul Smita Jyoti
- Department of Zoology, Section of Genetics, Drosophila Transgenic Laboratory, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Ambreen Fatima
- Department of Zoology, Section of Genetics, Drosophila Transgenic Laboratory, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Wasi Khan
- Department of Physics, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Braj Raj Singh
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, GualPahari, Gurgaon, Haryana, India
| | - A. H. Naqvi
- Interdisciplinary Nanotechnology Centre, Aligarh Muslim University, Aligarh, India
| | - Yasir Hasan Siddique
- Department of Zoology, Section of Genetics, Drosophila Transgenic Laboratory, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Sauerbier A, Cova I, Rosa-Grilo M, Taddei RN, Mischley LK, Chaudhuri KR. Treatment of Nonmotor Symptoms in Parkinson's Disease. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2017; 132:361-379. [PMID: 28554415 DOI: 10.1016/bs.irn.2017.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonmotor symptoms (NMS) are integral to Parkinson's disease (PD) and the management can often be challenging. In spite of the growing evidence that NMS have a key impact on the quality of life of patients and caregivers, most clinical trials still focus on motor symptoms as primary outcomes. As a consequence strong evidence-based treatment recommendations for NMS occurring in PD are spare. In this chapter, the current data addressing the treatment of major NMS such as sleep, cognitive and autonomic dysfunction, and depression and anxiety are described.
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Affiliation(s)
- Anna Sauerbier
- King's College London and King's College Hospital, London, United Kingdom.
| | - Ilaria Cova
- Center for Research and Treatment on Cognitive Dysfunctions, Institute of Clinical Neurology, Luigi Sacco' Hospital, University of Milan, Milan, Italy
| | - Miguel Rosa-Grilo
- King's College London and King's College Hospital, London, United Kingdom
| | - Raquel N Taddei
- King's College London and King's College Hospital, London, United Kingdom
| | - Laurie K Mischley
- Bastyr University Research Institute, Kenmore, WA, United States; UW Graduate Program in Nutritional Sciences, Seattle, WA, United States; University of Washington (UW), Seattle, WA, United States
| | - K Ray Chaudhuri
- National Parkinson Foundation International Centre of Excellence, Kings College and Kings College Hospital, London, United Kingdom; Maurice Wohl Clinical Neuroscience Institute, Kings College, London, United Kingdom; National Institute for Health Research (NIHR) Mental Health Biomedical Research Centre (BRC) and Dementia Unit at South London and Maudsley NHS Foundation Trust, London, United Kingdom
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Priapism and Hypersexuality Associated With Rotigotine in an Elderly Parkinsonian Patient. Clin Neuropharmacol 2016; 39:162-3. [DOI: 10.1097/wnf.0000000000000157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Daytime apomorphine infusion combined with transdermal Rotigotine patch therapy is tolerated at 2 years: A 24-h treatment option in Parkinson's disease. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.baga.2013.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Abstract
Dopamine receptor agonists are indicated for the symptomatic treatment of early, moderate or advanced Parkinson's disease as well as for the reduction of levodopa-related motor complications. Ergolinic dopamine agonists, such as bromocriptine or pergolide, were initially developed and marketed, and then non-ergolinic dopamine agonists, such as pramipexole and ropinirole, were introduced, reducing the risk of drug-induced fibrotic reactions. Once-daily, controlled-release oral and transdermal formulations have been developed aiming at providing more stable 24-hour plasma drug concentrations and more convenient administration. A disease-modifying effect of dopamine agonists has not been demonstrated clinically. As with any other drug, dopamine agonists can also cause adverse drug reactions, which can be related or unrelated to dopaminergic hyperactivation. Dopaminergic reactions include nausea, hallucinations, confusion and orthostatic hypotension, among others, which were readily identified in pre-marketing clinical trials. During post-marketing surveillance, important adverse reactions were identified, such as daytime somnolence, impulse-control disorders and heart valve fibrosis. Other issues, including the efficacy of dopamine agonists for the treatment of non-motor symptoms, remain under evaluation.
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Affiliation(s)
- Santiago Perez-Lloret
- Department of Clinical Pharmacology and Neurosciences, Hospital and University of Toulouse and INSERM CIC9023 and UMR 825, Toulouse, France
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Abstract
Considerable advances made in defining the aetiology, pathogenesis, and pathology of Parkinson's disease (PD) have resulted in the development and rapid expansion of the pharmacopoeia available for treatment. Anticholinergics were used before the introduction of levodopa which is now the drug most commonly used. Dopamine agonists are effective when used alone or as an adjunct to levodopa, while monoamine oxidase B inhibitors improve motor function in early and advanced PD. However, treatment mainly addresses the dopaminergic features of the disease and leaves its progressive course unaffected; the drug treatment available for the management of non-motor symptoms is limited. This article seeks to set current treatment options in context, review emerging and novel drug treatments for PD, and assess the prospects for disease modification. Surgical therapies are not considered.
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Affiliation(s)
- A H V Schapira
- University Department of Clinical Neurosciences, Royal Free and University College Medical School, London NW3 2PF, UK.
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Stiasny-Kolster K, Benes H, Peglau I, Hornyak M, Holinka B, Wessel K, Emser W, Leroux M, Kohnen R, Oertel WH. Effective cabergoline treatment in idiopathic restless legs syndrome. Neurology 2004; 63:2272-9. [PMID: 15623686 DOI: 10.1212/01.wnl.0000147297.51023.c8] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To assess the efficacy and safety of the dopamine agonist cabergoline (CAB) in patients with restless legs syndrome (RLS). METHODS Patients with moderate to severe RLS were randomized into four groups receiving placebo, 0.5 mg, 1 mg, or 2 mg CAB once daily in a double-blind, placebo-controlled, multicenter dose-finding trial followed by an open long-term extension trial of 47 weeks. Efficacy was assessed with the RLS-6 scales and International RLS Study Group severity scale (IRLS). RESULTS A total of 85 patients (age 56 +/- 10 years, 71% females) were treated. Severity of RLS-6 scale symptoms during the night (the primary endpoint) was markedly improved by all CAB doses compared to placebo (placebo: -1.4 +/- 3.1, 0.5 mg CAB: -4.2 +/- 3.0 [p = 0.0082], 1.0 mg CAB: -4.0 +/- 2.9 [p = 0.0040], 2.0 mg CAB: -4.8 +/- 3.7 [p = 0.0026]). Similar results were found for the RLS severity at bedtime and during the day, IRLS, and satisfaction with sleep. A stable, clinically relevant improvement was achieved in all efficacy measures (severity during the night: change between last assessment and baseline: -5.6 +/- 2.5, rate of remission: 71.2%) throughout 1 year with a mean CAB dose of 2.2 mg per day. During long-term treatment, 6 of 66 treated patients were affected (n = 2) or possibly affected (n = 4) by mild augmentation. Under CAB therapy up to 1 year, 11 of 85 patients discontinued treatment due to a drug-related adverse event. CONCLUSIONS Cabergoline is an efficacious and well-tolerated option for the treatment of restless legs symptoms during the night and the day.
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Thanvi BR, Lo TCN. Long term motor complications of levodopa: clinical features, mechanisms, and management strategies. Postgrad Med J 2004; 80:452-8. [PMID: 15299154 PMCID: PMC1743071 DOI: 10.1136/pgmj.2003.013912] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Levodopa is the most effective symptomatic treatment of Parkinson's disease. However, after an initial period of dramatic benefit, several limitations become apparent including, "dopa resistant" motor symptoms (postural abnormalities, freezing episodes, speech impairment), "dopa resistant" non-motor signs (autonomic dysfunction, mood and cognitive impairment, etc), and/or drug related side effects (especially psychosis, motor fluctuations, and dyskinesias). Motor complications include fluctuations, dyskinesias, and dystonias. They can be very disabling and difficult to treat. Therefore, strategies should ideally be developed to prevent them. Though mechanisms underlying motor complications are only partially understood, recent work has revealed the importance of pulsatile stimulation of postsynaptic dopamine receptors and the disease severity. As a result of intermittent stimulation there occurs a cascade of changes in cell signalling leading to upregulation of the N-methyl-D-aspartate subtype of gamma-aminobutryric acid-ergic neurones. Modified preparations of levodopa (controlled release preparations, liquid levodopa), catecholamine-o-methyltransferase inhibitors, dopamine agonists, amantidine, and various neurosurgical approaches have been used in the prevention and/or treatment of motor complications. Current management of motor complications is less than satisfactory. With better understanding of the pathogenetic mechanisms, it is hoped that future therapeutic strategies will provide a safer and targeted treatment.
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Affiliation(s)
- B R Thanvi
- Department of Integrated Medicine, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Infirmary Squire, Leicester LE1 5WW, UK.
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