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Wang Y, Su Y, Zhao K, Huo D, Du Z, Wang Z, Xie H, Liu L, Jin Q, Ren X, Chen X, Zhang D. A deep learning drug screening framework for integrating local-global characteristics: A novel attempt for limited data. Heliyon 2024; 10:e34244. [PMID: 39130417 PMCID: PMC11315141 DOI: 10.1016/j.heliyon.2024.e34244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/31/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
At the beginning of the "Disease X" outbreak, drug discovery and development are often challenged by insufficient and unbalanced data. To address this problem and maximize the information value of limited data, we propose a drug screening model, LGCNN, based on convolutional neural network (CNN), which enables rapid drug screening by integrating features of drug molecular structures and drug-target interactions at both local and global (LG) levels. Experimental results show that LGCNN exhibits better performance compared to other state-of-the-art classification methods under limited data. In addition, LGCNN was applied to anti-SARS-CoV-2 drug screening to realize therapeutic drug mining against COVID-19. LGCNN transcends the limitations of traditional models for predicting interactions between single drug targets and shows new advantages in predicting multi-target drug-target interactions. Notably, the cross-coronavirus generalizability of the model is also implied by the analysis of targets, drugs, and mechanisms in the prediction results. In conclusion, LGCNN provides new ideas and methods for rapid drug screening in emergency situations where data are scarce.
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Affiliation(s)
- Ying Wang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yangguang Su
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Kairui Zhao
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Diwei Huo
- The Fourth Hospital of Harbin Medical University, No.37 Yiyuan Street, Harbin, Heilongjiang, 150001, China
| | - Zhenshun Du
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Zhiju Wang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Hongbo Xie
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Lei Liu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Qing Jin
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xuekun Ren
- College of Mathematics of Harbin Institute of Technology, No.92 Xidazhi Street, Harbin, Heilongjiang, 150001, China
| | - Xiujie Chen
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Denan Zhang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
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Ahmad SS, Kamal MA. Current Updates on the Regulation of Beta-Secretase Movement as a Potential Restorative Focus for Management of Alzheimer's Disease. Protein Pept Lett 2019; 26:579-587. [DOI: 10.2174/0929866526666190405125334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/16/2019] [Accepted: 03/17/2019] [Indexed: 11/22/2022]
Abstract
The most recent decade was described by a developing awareness about the
seriousness of dementia in the field of age-related people. Among the dementias, Alzheimer's
assumes a plentiful role as a result of its amazingly high rate and casualty. A few
pharmacological procedures have been attempted yet at the same time now, Alzheimer continues
being an untreatable malady. The collection of Aβ in the brain is an early poisonous occasion in
the pathogenesis of Alzheimer's disease, which is the most widely recognized type of dementia
correlated with plaques and tangles within the brain. However, the mechanism of the
intraneuronal direction of BACE1 is poorly understood. AD is caused by mutations in one of the
genes that encoding APP, presenilins 1 and 2. Most of the mutations in these genes increase
Aβ42 production. Numerous receptors are associated with initiating Aβ transport and clearance.
Among them, RAGE is an influx transport receptor that binds soluble Aβ and mediates
pathophysiological cellular responses. RAGE additionally intervenes the vehicle of plasma Aβ
over the blood-brain barrier. LRP-1 functions as a clearance receptor for Aβ at the blood-brain
barrier. The regulation of beta-secretase movement is being explored as a potential restorative
focus for treating AD.
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Affiliation(s)
- Syed Sayeed Ahmad
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, India
| | - Mohammad Amjad Kamal
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Zhang M, Wu Q, Yao X, Zhao J, Zhong W, Liu Q, Xiao S. Xanthohumol inhibits tau protein aggregation and protects cells against tau aggregates. Food Funct 2019; 10:7865-7874. [DOI: 10.1039/c9fo02133g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Xanthohumol is shown to interact with tau protein and inhibit its aggregation.
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Affiliation(s)
- Mohan Zhang
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- China
| | - Qiuping Wu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- China
| | - Xuanbao Yao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- China
| | - Junyi Zhao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- China
| | - Weicong Zhong
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- China
| | - Qiong Liu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- China
| | - Shifeng Xiao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- China
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Abstract
Recent advances in understanding of the molecular biology of prion diseases and improved clinical diagnostic techniques might allow researchers to think about therapeutic trials in Creutzfeldt-Jakob disease (CJD) patients. Some attempts have been made in the past and various compounds have been tested in single case reports and patient series. Controlled trials are rare. However, in the past few years, it has been demonstrated that clinical trials are feasible. The clinicians might face several specific problems when evaluating the efficacy of the drug in CJD, such as rareness of the disease, lack of appropriate preclinical tests and heterogeneous clinical presentation in humans. These problems have to be carefully addressed in future.
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Affiliation(s)
- Saima Zafar
- Clinical Dementia Center and German Center for Neurodegenerative Diseases, Department of Neurology, Georg-August University, University Medical Center Göttingen, Göttingen, Germany; Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Aneeqa Noor
- Clinical Dementia Center and German Center for Neurodegenerative Diseases, Department of Neurology, Georg-August University, University Medical Center Göttingen, Göttingen, Germany
| | - Inga Zerr
- Clinical Dementia Center and German Center for Neurodegenerative Diseases, Department of Neurology, Georg-August University, University Medical Center Göttingen, Göttingen, Germany.
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Chen GF, Xu TH, Yan Y, Zhou YR, Jiang Y, Melcher K, Xu HE. Amyloid beta: structure, biology and structure-based therapeutic development. Acta Pharmacol Sin 2017; 38:1205-1235. [PMID: 28713158 PMCID: PMC5589967 DOI: 10.1038/aps.2017.28] [Citation(s) in RCA: 1001] [Impact Index Per Article: 143.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/02/2017] [Indexed: 12/12/2022] Open
Abstract
Amyloid beta peptide (Aβ) is produced through the proteolytic processing of a transmembrane protein, amyloid precursor protein (APP), by β- and γ-secretases. Aβ accumulation in the brain is proposed to be an early toxic event in the pathogenesis of Alzheimer's disease, which is the most common form of dementia associated with plaques and tangles in the brain. Currently, it is unclear what the physiological and pathological forms of Aβ are and by what mechanism Aβ causes dementia. Moreover, there are no efficient drugs to stop or reverse the progression of Alzheimer's disease. In this paper, we review the structures, biological functions, and neurotoxicity role of Aβ. We also discuss the potential receptors that interact with Aβ and mediate Aβ intake, clearance, and metabolism. Additionally, we summarize the therapeutic developments and recent advances of different strategies for treating Alzheimer's disease. Finally, we will report on the progress in searching for novel, potentially effective agents as well as selected promising strategies for the treatment of Alzheimer's disease. These prospects include agents acting on Aβ, its receptors and tau protein, such as small molecules, vaccines and antibodies against Aβ; inhibitors or modulators of β- and γ-secretase; Aβ-degrading proteases; tau protein inhibitors and vaccines; amyloid dyes and microRNAs.
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Affiliation(s)
- Guo-Fang Chen
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ting-Hai Xu
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yan Yan
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yu-Ren Zhou
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Jiang
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - H Eric Xu
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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Awasthi M, Singh S, Pandey VP, Dwivedi UN. Alzheimer's disease: An overview of amyloid beta dependent pathogenesis and its therapeutic implications along with in silico approaches emphasizing the role of natural products. J Neurol Sci 2016; 361:256-71. [DOI: 10.1016/j.jns.2016.01.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 01/02/2016] [Accepted: 01/04/2016] [Indexed: 01/09/2023]
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Dall'Ara P, Iulini B, Botto L, Filipe J, Martino PA, Pintore MD, Gazzuola P, Mazza M, Dagrada M, Ingravalle F, Casalone C, Palestini P, Poli G. Diets with different lipid contents do not modify the neuronal membrane lipid raft profile in a scrapie murine model. Life Sci 2016; 144:226-33. [PMID: 26655166 DOI: 10.1016/j.lfs.2015.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 11/26/2015] [Accepted: 12/02/2015] [Indexed: 10/22/2022]
Abstract
UNLABELLED In Transmissible Spongiform Encephalopathies (TSEs), the localization of the prion protein in the neuronal membrane lipid rafts (LR) seems to play a role in sustaining the protein misfolding. Changes in membrane properties, due to altered lipid composition, affect their organization and interaction between lipids and protein therein, and consequently also membrane resident protein functionality; dietary polyunsaturated fatty acids (PUFAs), gangliosides and cholesterol seem to influence these processes. AIMS In this work, the influence of administration of different feed, able to change the composition of lipid membrane, on the clinical progression of prion disease was studied. MAIN METHODS The activity of three diets (hyperlipidic with 6% fats; hypolipidic with 0.1% fats; and purified with 4% fats) was tested in CD1 mouse model experimentally infected with RML scrapie strain. Presence and distribution of typical central nervous system (CNS) lesions and deposits of PrP(sc) were evaluated by histopathological analysis and immunohistochemistry. Analysis of lipids was performed in homogenate and insoluble brain fraction of the neuronal membrane rich in LR. KEY FINDINGS Results show that a diet with a different lipid level has not a significant role in the development of the scrapie disease. All infected mice fed with different diets died in the same time span. Histology, immunohistochemistry, and neuropathological analyses of the infected brains did not show significant differences between animals subjected to different diets. SIGNIFICANCE Independently of the diet, the infection induced a significant modification of the lipid composition in homogenates, and a less noticeable one in insoluble brain fraction.
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Affiliation(s)
- Paola Dall'Ara
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy.
| | - Barbara Iulini
- CEA, Italian Reference Laboratory for TSEs, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Laura Botto
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Joel Filipe
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
| | - Piera Anna Martino
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
| | - Maria Domenica Pintore
- CEA, Italian Reference Laboratory for TSEs, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Paola Gazzuola
- CEA, Italian Reference Laboratory for TSEs, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Maria Mazza
- CEA, Italian Reference Laboratory for TSEs, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Massimo Dagrada
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
| | - Francesco Ingravalle
- CEA, Italian Reference Laboratory for TSEs, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Cristina Casalone
- CEA, Italian Reference Laboratory for TSEs, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
| | - Paola Palestini
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Giorgio Poli
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
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Potential therapeutic strategies for Alzheimer's disease targeting or beyond β-amyloid: insights from clinical trials. BIOMED RESEARCH INTERNATIONAL 2014; 2014:837157. [PMID: 25136630 PMCID: PMC4124758 DOI: 10.1155/2014/837157] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 01/25/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with two hallmarks: β-amyloid plagues and neurofibrillary tangles. It is one of the most alarming illnesses to elderly people. No effective drugs and therapies have been developed, while mechanism-based explorations of therapeutic approaches have been intensively investigated. Outcomes of clinical trials suggested several pitfalls in the choice of biomarkers, development of drug candidates, and interaction of drug-targeted molecules; however, they also aroused concerns on the potential deficiency in our understanding of pathogenesis of AD, and ultimately stimulated the advent of novel drug targets tests. The anticipated increase of AD patients in next few decades makes development of better therapy an urgent issue. Here we attempt to summarize and compare putative therapeutic strategies that have completed clinical trials or are currently being tested from various perspectives to provide insights for treatments of Alzheimer's disease.
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Golde TE, Koo EH, Felsenstein KM, Osborne BA, Miele L. γ-Secretase inhibitors and modulators. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1828:2898-907. [PMID: 23791707 PMCID: PMC3857966 DOI: 10.1016/j.bbamem.2013.06.005] [Citation(s) in RCA: 215] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/04/2013] [Indexed: 12/11/2022]
Abstract
γ-Secretase is a fascinating, multi-subunit, intramembrane cleaving protease that is now being considered as a therapeutic target for a number of diseases. Potent, orally bioavailable γ-secretase inhibitors (GSIs) have been developed and tested in humans with Alzheimer's disease (AD) and cancer. Preclinical studies also suggest the therapeutic potential for GSIs in other disease conditions. However, due to inherent mechanism based-toxicity of non-selective inhibition of γ-secretase, clinical development of GSIs will require empirical testing with careful evaluation of benefit versus risk. In addition to GSIs, compounds referred to as γ-secretase modulators (GSMs) remain in development as AD therapeutics. GSMs do not inhibit γ-secretase, but modulate γ-secretase processivity and thereby shift the profile of the secreted amyloid β peptides (Aβ) peptides produced. Although GSMs are thought to have an inherently safe mechanism of action, their effects on substrates other than the amyloid β protein precursor (APP) have not been extensively investigated. Herein, we will review the current state of development of GSIs and GSMs and explore pertinent biological and pharmacological questions pertaining to the use of these agents for select indications. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Todd E Golde
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
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Poli G, Corda E, Martino PA, Dall'ara P, Bareggi SR, Bondiolotti G, Iulini B, Mazza M, Casalone C, Hwang SH, Hammock BD, Inceoglu B. Therapeutic activity of inhibition of the soluble epoxide hydrolase in a mouse model of scrapie. Life Sci 2013; 92:1145-50. [PMID: 23651659 DOI: 10.1016/j.lfs.2013.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/05/2013] [Accepted: 04/27/2013] [Indexed: 01/08/2023]
Abstract
AIMS The misfolding and the aggregation of specific proteins are key features of neurodegenerative diseases, specifically Transmissible Spongiform Encephalopathies (TSEs). In TSEs, neuronal loss and inflammation are associated with the accumulation of the misfolded isoform (PrP(sc)) of the cellular prion protein (PrP(c)). Therefore we tested the hypothesis that augmenting a natural anti-inflammatory pathway mediated by epoxygenated fatty acids (EpFAs) will delay lethality. EpFAs are highly potent but enzymatically labile molecules produced by the actions of a number of cytochrome P450 enzymes. Stabilization of these bioactive lipids by inhibiting their degradation mediated by the soluble epoxide hydrolase (sEH) results in potent anti-inflammatory effects in multiple disease models. MAIN METHODS Mice were infected with the mouse-adapted RML strain of scrapie by intracerebral or intraperitoneal routes. Animals received the sEH inhibitor, by oral route, administrated in drinking water or vehicle (PEG400). Infected mice were euthanized at a standard clinical end point. Histopathological, immunohistochemical and Western blot analyses of brain tissue confirmed the presence of pathology related to prion infection. KEY FINDINGS Oral administration of the sEHI did not affect the very short survival time of the intracerebral prion infection group. However, mice infected by intraperitoneal route and treated with t-AUCB survived significantly longer than the control group mice (p<0.001). SIGNIFICANCE These findings support the idea that inhibition of sEH or augmentation of the natural EpFA signaling in the brain offers a potential and different route to understand prion diseases and may become a therapeutic strategy for diseases involving neuroinflammation.
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Affiliation(s)
- Giorgio Poli
- Department of Veterinary Science and Public Health, Faculty of Veterinary Medicine, University of Milan, Milan, Italy
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