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Zheng S, Zhang C, Chen Y, Chen M. Graph and Multi-Level Sequence Fusion Learning for Predicting the Molecular Activity of BACE-1 Inhibitors. Int J Mol Sci 2025; 26:1681. [PMID: 40004143 PMCID: PMC11855840 DOI: 10.3390/ijms26041681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 02/12/2025] [Accepted: 02/14/2025] [Indexed: 02/27/2025] Open
Abstract
The development of BACE-1 (β-site amyloid precursor protein cleaving enzyme 1) inhibitors is a crucial focus in exploring early treatments for Alzheimer's disease (AD). Recently, graph neural networks (GNNs) have demonstrated significant advantages in predicting molecular activity. However, their reliance on graph structures alone often neglects explicit sequence-level semantic information. To address this limitation, we proposed a Graph and multi-level Sequence Fusion Learning (GSFL) model for predicting the molecular activity of BACE-1 inhibitors. Firstly, molecular graph structures generated from SMILES strings were encoded using GNNs with an atomic-level characteristic attention mechanism. Next, substrings at functional group, ion level, and atomic level substrings were extracted from SMILES strings and encoded using a BiLSTM-Transformer framework equipped with a hierarchical attention mechanism. Finally, these features were fused to predict the activity of BACE-1 inhibitors. A dataset of 1548 compounds with BACE-1 activity measurements was curated from the ChEMBL database. In the classification experiment, the model achieved an accuracy of 0.941 on the training set and 0.877 on the test set. For the test set, it delivered a sensitivity of 0.852, a specificity of 0.894, a MCC of 0.744, an F1-score of 0.872, a PRC of 0.869, and an AUC of 0.915. Compared to traditional computer-aided drug design methods and other machine learning algorithms, the proposed model can effectively improve the accuracy of the molecular activity prediction of BACE-1 inhibitors and has a potential application value.
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Affiliation(s)
- Shaohua Zheng
- College of Physics and Information Engineering, Fuzhou University, Fuzhou 350108, China
| | - Changwang Zhang
- College of Physics and Information Engineering, Fuzhou University, Fuzhou 350108, China
| | - Youjia Chen
- College of Physics and Information Engineering, Fuzhou University, Fuzhou 350108, China
| | - Meimei Chen
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
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Ragheb MA, Abdelrashid HE, Elzayat EM, Abdelhamid IA, Soliman MH. Novel cyanochalcones as potential anticancer agents: apoptosis, cell cycle arrest, DNA binding, and molecular docking studies. J Biomol Struct Dyn 2024:1-19. [PMID: 38373066 DOI: 10.1080/07391102.2024.2316764] [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: 10/09/2023] [Accepted: 02/02/2024] [Indexed: 02/21/2024]
Abstract
In the light of anticancer drug discovery and development, a new series of cyanochalcones incorporating indole moiety (5a-g) were efficiently synthesized and characterized by different spectral analysis. MTT assay was used to evaluate the antiproliferative activity of the synthesized compounds towards different cancer cells (Hela, MDA-MB-231, A375, and A549) in parallel with normal cells (HSF). Trimethoxy and diethoxy-containing derivatives (5d and 5e) displayed the most selective cytotoxic activities against cervical Hela cells with IC50 values of 8.29 and 11.82 µM, respectively, with great safety pattern toward normal HSF cells (Selectivity index: 21.3 and 13.9, respectively). Therefore, 5d and 5e were chosen to study their effects on apoptosis, cell cycle arrest, and migration of Hela cells using flow cytometric analysis and wound healing assay. They induced apoptosis and cell cycle arrest at the S phase and impaired migration of HeLa cells. Regarding their effects on the expression profile of crucial genes related to the potential anticancer activities, 5d and 5e remarkably upregulated caspase 3 and Beclin1 and downregulated cyclin A1, CDK2, CDH2, MMP9, and HIF1A using qRT-PCR and ELISA techniques. UV-Vis spectral measurement demonstrated the ability of 5d and 5e to bind CT-DNA efficiently with Kb values of 3.7 × 105 and 1 × 105 M-1, respectively. Moreover, in silico molecular docking was performed to assess the binding affinities of the compounds toward the active sites of Bcl2, CDK2, and DNA. Therefore, cyanochalcones 5d and 5e might be promising anticancer agents and could offer a scientific basis for intensive research into cancer chemotherapy.
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Affiliation(s)
- Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
| | - Hanan E Abdelrashid
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
| | - Emad M Elzayat
- Biotechnology Department, Faculty of Science, Cairo University, Giza, Egypt
| | | | - Marwa H Soliman
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
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Satpathy R. Quantitative Structure-Activity Relationship (QSAR) Study of Potential Phytochemicals for the Development of Drugs Against Neurological Diseases. ADVANCES IN MEDICAL DIAGNOSIS, TREATMENT, AND CARE 2023:1-21. [DOI: 10.4018/978-1-6684-9463-9.ch001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
Abstract
Neurological diseases have recently evolved into a global concern and are commonly observed in elderly populations. Common examples of these diseases are Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). The remarkable application of the computational approach in biological sciences has expedited the drug development process from natural compounds that uncover opportunities to develop new medications. In the computer-aided drug design (CADD) process, the quantitative structure-activity relationship (QSAR) method is crucial in molecule screening and lead optimization. This chapter discusses the potential phytochemicals used to treat these diseases. The process of CADD, along with QSAR methods and the importance of blood-brain barriers (BBB), has been elaborated. The targets of AD and the QSAR analysis of the phytochemicals have been discussed by taking AD as a case study with the challenges of treating these diseases.
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Structure-Based Drug Design of Novel Piperazine Containing Hydrazone Derivatives as Potent Alzheimer Inhibitors: Molecular Docking and Drug Kinetics Evaluation. BRAIN DISORDERS 2022. [DOI: 10.1016/j.dscb.2022.100041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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5
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Gorzalczany SB, Rodriguez Basso AG. Strategies to apply 3Rs in preclinical testing. Pharmacol Res Perspect 2021; 9:e00863. [PMID: 34609088 PMCID: PMC8491455 DOI: 10.1002/prp2.863] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Animal experimentation has been fundamental in biological and biomedical research. To guarantee the maximum quality, efficacy and/or safety of products intended for the use in humans in vivo testing is necessary; however, for over 60 years, alternative methods have been developed in response to the necessity to reduce the number of animals used in experimentation, to guarantee their welfare; resorting to animal models only when strictly necessary. The three Rs (Replacement, Reduction, and Refinement), seek to ensure the rational and respectful use of laboratory animals and maintain an adequate projection in terms of bioethical considerations. This article describes different approaches to apply 3Rs in preclinical experimentation for either research or regulatory purposes.
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Affiliation(s)
- Susana B. Gorzalczany
- Universidad de Buenos AiresFacultad de Farmacia y Bioquímica, Pharmacology DepartmentBuenos AiresArgentina
| | - Angeles G. Rodriguez Basso
- Universidad de Buenos AiresFacultad de Farmacia y Bioquímica, Pharmacology DepartmentBuenos AiresArgentina
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6
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Olasupo SB, Uzairu A, Shallangwa GA, Uba S. Computer-aided drug design and in silico pharmacokinetics predictions of some potential antipsychotic agents. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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7
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Olasupo SB, Uzairu A, Shallangwa GA, Uba S. Unveiling novel inhibitors of dopamine transporter via in silico drug design, molecular docking, and bioavailability predictions as potential antischizophrenic agents. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00198-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The inhibition of dopamine transporter is known to play a significant role in the treatment of schizophrenia-related and other mental disorders. In a continuing from our previous study, computational drug design approach, molecular docking simulation, and pharmacokinetics study were explored for the identification of novel inhibitors dopamine transporter as potential Antischizophrenic agents. Consequently, thirteen (13) new inhibitors of dopamine transporter were designed by selecting the molecule with serial number 39 from our previous study as the template molecule because it exhibits good pharmacological attributes.
Results
Molecular docking simulation results revealed excellent molecular interactions between the protein target (PDB: 4m48) and the ligands (designed inhibitors) with major interactions that involved hydrogen bonding and hydrophobic interactions. Also, some of the designed inhibitors displayed a superior binding affinity range from − 10.0 to − 10.7 kcal/mol compared to the referenced drug (Lumateperone) with a binding affinity of − 9.7 kcal/mol. Computed physicochemical parameters showed that none of the designed inhibitors including the referenced drug violate Lipinski’s rule of five indicating that all the designed inhibitors would be orally bioavailable as potential drug candidates. Similarly, the ADMET/pharmacokinetics evaluations of some designed inhibitors revealed that they possessed good absorption, distribution, metabolism and excretion properties and none of the inhibitors is neither carcinogens nor toxic toward human ether-a-go-go related gene (hERG I) inhibitor or skin sensitization. Likewise, the BOILED-Egg graphics unveils that all the designed inhibitors demonstrate a high probability to be absorbed by the human gastrointestinal tract and could permeate into the brain. Besides, the predicted bioactive parameters suggested that all the selected inhibitors would be active as drug candidates. Furthermore, the synthetic accessibility scores for all the selected inhibitors and referenced drug lied within the easy zone (i.e., between 1–4) with their computed values range from 2.55 to 3.92, this implies that all the selected inhibitors would be very easy to synthesize in the laboratory.
Conclusions
Hence, all the designed inhibitors having shown excellent pharmacokinetics properties and good bioavailabilities attributes with remarkable biochemical interactions could be developed and optimized as novel Antischizophrenic agents after the conclusion of other experimental investigations.
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Ebrahim-Habibi A, Kashani-Amin E, Larijani B. Modeling and simulation in medical sciences: an overview of specific applications based on research experience in EMRI (Endocrinology and Metabolism Research Institute of Tehran University of Medical Sciences). J Diabetes Metab Disord 2021:1-7. [PMID: 33500880 PMCID: PMC7821172 DOI: 10.1007/s40200-020-00706-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 01/31/2023]
Abstract
The concomitant use of various types of models (in silico, in vitro, and in vivo) has been exemplified here within the context of biomedical researches performed in the Endocrinology and Metabolism Research Institute (EMRI) of Tehran University of Medical Sciences. Two main research aeras have been discussed: the search for new small molecules as therapeutics for diabetes and related metabolic conditions, and diseases related to protein aggregation. Due to their multidisciplinary nature, the majority of these studies have needed the collaboration of different specialties. In both cases, a brief overview of the subject is provided through literature examples, and sequential use of these methods is described.
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Affiliation(s)
- Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Jalal-al-Ahmad Street, Chamran Highway, 1411713137 Tehran, Iran
| | - Elaheh Kashani-Amin
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Jalal-al-Ahmad Street, Chamran Highway, 1411713137 Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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9
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Lu X, Jia C, Gao J, Wang R, Zhang L, Sun Q, Huang J. Structure–activity relationship and molecular docking analysis of cysteine‐containing dipeptides as antioxidant and ACE inhibitory. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xin Lu
- Research Center for Agricultural and Sideline Products Processing Henan Academy of Agricultural Sciences 116 Park Road Zhengzhou450002China
| | - Cong Jia
- Research Center for Agricultural and Sideline Products Processing Henan Academy of Agricultural Sciences 116 Park Road Zhengzhou450002China
| | - Jinhong Gao
- Research Center for Agricultural and Sideline Products Processing Henan Academy of Agricultural Sciences 116 Park Road Zhengzhou450002China
| | - Ruidan Wang
- Research Center for Agricultural and Sideline Products Processing Henan Academy of Agricultural Sciences 116 Park Road Zhengzhou450002China
| | - Lixia Zhang
- Research Center for Agricultural and Sideline Products Processing Henan Academy of Agricultural Sciences 116 Park Road Zhengzhou450002China
| | - Qiang Sun
- Research Center for Agricultural and Sideline Products Processing Henan Academy of Agricultural Sciences 116 Park Road Zhengzhou450002China
| | - Jinian Huang
- Research Center for Agricultural and Sideline Products Processing Henan Academy of Agricultural Sciences 116 Park Road Zhengzhou450002China
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10
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Wu F, Zhou Y, Li L, Shen X, Chen G, Wang X, Liang X, Tan M, Huang Z. Computational Approaches in Preclinical Studies on Drug Discovery and Development. Front Chem 2020; 8:726. [PMID: 33062633 PMCID: PMC7517894 DOI: 10.3389/fchem.2020.00726] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
Because undesirable pharmacokinetics and toxicity are significant reasons for the failure of drug development in the costly late stage, it has been widely recognized that drug ADMET properties should be considered as early as possible to reduce failure rates in the clinical phase of drug discovery. Concurrently, drug recalls have become increasingly common in recent years, prompting pharmaceutical companies to increase attention toward the safety evaluation of preclinical drugs. In vitro and in vivo drug evaluation techniques are currently more mature in preclinical applications, but these technologies are costly. In recent years, with the rapid development of computer science, in silico technology has been widely used to evaluate the relevant properties of drugs in the preclinical stage and has produced many software programs and in silico models, further promoting the study of ADMET in vitro. In this review, we first introduce the two ADMET prediction categories (molecular modeling and data modeling). Then, we perform a systematic classification and description of the databases and software commonly used for ADMET prediction. We focus on some widely studied ADMT properties as well as PBPK simulation, and we list some applications that are related to the prediction categories and web tools. Finally, we discuss challenges and limitations in the preclinical area and propose some suggestions and prospects for the future.
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Affiliation(s)
- Fengxu Wu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China
| | - Yuquan Zhou
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Langhui Li
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianhuan Shen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Ganying Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Xiaoqing Wang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Xianyang Liang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Mengyuan Tan
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Research Platform Service Management Center, Dongguan, China
- Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China
- Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
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11
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Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020; 8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
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Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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12
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Chainoglou E, Hadjipavlou-Litina D. Curcumin in Health and Diseases: Alzheimer's Disease and Curcumin Analogues, Derivatives, and Hybrids. Int J Mol Sci 2020; 21:ijms21061975. [PMID: 32183162 PMCID: PMC7139886 DOI: 10.3390/ijms21061975] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/28/2022] Open
Abstract
Worldwide, Alzheimer’s disease (AD) is the most common neurodegenerative multifactorial disease influencing the elderly population. Nowadays, several medications, among them curcumin, are used in the treatment of AD. Curcumin, which is the principal component of Curcuma longa, has shown favorable effects forsignificantly preventing or treating AD. During the last decade, the scientific community has focused their research on the optimization of therapeutic properties and on the improvement of pharmacokinetic properties of curcumin. This review summarizes bibliographical data from 2009 to 2019 on curcumin analogues, derivatives, and hybrids, as well as their therapeutic, preventic, and diagnostic applications in AD. Recent advances in the field have revealed that the phenolic hydroxyl group could contribute to the anti-amyloidogenic activity. Phenyl methoxy groups seem to contribute to the suppression of amyloid-β peptide (Aβ42) and to the suppression of amyloid precursor protein (APP) andhydrophobic interactions have also revealed a growing role. Furthermore, flexible moieties, at the linker, are crucial for the inhibition of Aβ aggregation. The inhibitory activity of derivatives is increased with the expansion of the aromatic rings. The promising role of curcumin-based compounds in diagnostic imaging is highlighted. The keto-enol tautomerism seems to be a novel modification for the design of amyloid-binding agents. Molecular docking results, (Q)SAR, as well as in vitro and in vivo tests highlight the structures and chemical moieties that are correlated with specific activity. As a result, the knowledge gained from the existing research should lead to the design and synthesis ofinnovative and multitargetedcurcumin analogues, derivatives, or curcumin hybrids, which would be very useful drug and tools in medicine for both diagnosis and treatment of AD.
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13
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Cheminformatic modelling of β-amyloid aggregation inhibitory activity against Alzheimer's disease. Comput Biol Med 2020; 118:103658. [DOI: 10.1016/j.compbiomed.2020.103658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/06/2020] [Accepted: 02/08/2020] [Indexed: 11/21/2022]
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14
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Mouchlis VD, Melagraki G, Zacharia LC, Afantitis A. Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer's Therapeutics. Int J Mol Sci 2020; 21:E703. [PMID: 31973122 PMCID: PMC7038192 DOI: 10.3390/ijms21030703] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022] Open
Abstract
Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer's is the most common neurodegenerative disease and it can be caused by genetic and environmental risk factors. This review describes the amyloid-β and Tau hypotheses leading to amyloid plaques and neurofibrillary tangles, respectively which are the predominant pathways for the development of anti-Alzheimer's small molecule inhibitors. The function and structure of the druggable targets of these two pathways including β-secretase, γ-secretase, and Tau are discussed in this review article. Computer-Aided Drug Design including computational structure-based design and ligand-based design have been employed successfully to develop inhibitors for biomolecular targets involved in Alzheimer's. The application of computational molecular modeling for the discovery of small molecule inhibitors and modulators for β-secretase and γ-secretase is summarized. Examples of computational approaches employed for the development of anti-amyloid aggregation and anti-Tau phosphorylation, proteolysis and aggregation inhibitors are also reported.
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Affiliation(s)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, Vari 16672, Greece;
| | - Lefteris C. Zacharia
- Department of Life and Health Sciences, University of Nicosia, Nicosia 1700, Cyprus;
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus
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15
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Masand VH, El-Sayed NNE, Rastija V, Rathore MM, Karnaš M. Identification of prodigious and under-privileged structural features for RG7834 analogs as Hepatitis B virus expression inhibitor. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02455-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Roman DL, Roman M, Som C, Schmutz M, Hernandez E, Wick P, Casalini T, Perale G, Ostafe V, Isvoran A. Computational Assessment of the Pharmacological Profiles of Degradation Products of Chitosan. Front Bioeng Biotechnol 2019; 7:214. [PMID: 31552240 PMCID: PMC6743017 DOI: 10.3389/fbioe.2019.00214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/22/2019] [Indexed: 12/14/2022] Open
Abstract
Chitosan is a natural polymer revealing an increased potential to be used in different biomedical applications, including drug delivery systems, and tissue engineering. It implies the evaluation of the organism response to the biomaterial implantation. Low-molecular degradation products, the chito-oligomers, are resulting mainly from the influence of enzymes, which are found in the organism fluids. Within this study, we have performed the computational assessment of pharmacological profiles and toxicological effects on human health of small chito-oligomers with distinct molecular weights, deacetylation degrees, and acetylation patterns. Our approach is based on the fact that regulatory agencies and researchers in the drug development field rely on the use of modeling to predict biological effects and to guide decision making. To be considered as valid for regulatory purposes, every model that is used for predictions should be associated with a defined toxicological endpoint and has appropriate robustness and predictivity. Within this context, we have used FAF-Drugs4, SwissADME, and PreADMET tools to predict the oral bioavailability of chito-oligomers and SwissADME, PreADMET, and admetSAR2.0 tools to predict their pharmacokinetic profiles. The organs and genomic toxicities have been assessed using admetSAR2.0 and PreADMET tools but specific computational facilities have been also used for predicting different toxicological endpoints: Pred-Skin for skin sensitization, CarcinoPred-EL for carcinogenicity, Pred-hERG for cardiotoxicity, ENDOCRINE DISRUPTOME for endocrine disruption potential and Toxtree for carcinogenicity and mutagenicity. Our computational assessment showed that investigated chito-oligomers reflect promising pharmacological profiles and limited toxicological effects on humans, regardless of molecular weight, deacetylation degree, and acetylation pattern. According to our results, there is a possible inhibition of the organic anion transporting peptides OATP1B1 and/or OATP1B3, a weak potential of cardiotoxicity, a minor probability of affecting the androgen receptor, and phospholipidosis. Consequently, these results may be used to guide or to complement the existing in vitro and in vivo toxicity tests, to optimize biomaterials properties and to contribute to the selection of prototypes for nanocarriers.
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Affiliation(s)
- Diana Larisa Roman
- Advanced Environmental Research Laboratories, Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, Timisoara, Romania
| | - Marin Roman
- Advanced Environmental Research Laboratories, Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, Timisoara, Romania
| | - Claudia Som
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Technology and Society Laboratory, St. Gallen, Switzerland
| | - Mélanie Schmutz
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Technology and Society Laboratory, St. Gallen, Switzerland
| | - Edgar Hernandez
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Technology and Society Laboratory, St. Gallen, Switzerland
| | - Peter Wick
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Particles-Biology Interactions Laboratory, St. Gallen, Switzerland
| | - Tommaso Casalini
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Giuseppe Perale
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Vasile Ostafe
- Advanced Environmental Research Laboratories, Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, Timisoara, Romania
| | - Adriana Isvoran
- Advanced Environmental Research Laboratories, Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, Timisoara, Romania
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Synthesis of novel spiro-condensed 2-amino-4H-pyrans based on 1,2-benzoxathiin-4(3H)-one 2,2-dioxide. Chem Heterocycl Compd (N Y) 2019. [DOI: 10.1007/s10593-019-02450-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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