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Xu F, Yang Z, Wang L, Meng D, Long J. MESPool: Molecular Edge Shrinkage Pooling for hierarchical molecular representation learning and property prediction. Brief Bioinform 2023; 25:bbad423. [PMID: 38048081 PMCID: PMC10753536 DOI: 10.1093/bib/bbad423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/18/2023] [Accepted: 10/29/2023] [Indexed: 12/05/2023] Open
Abstract
Identifying task-relevant structures is important for molecular property prediction. In a graph neural network (GNN), graph pooling can group nodes and hierarchically represent the molecular graph. However, previous pooling methods either drop out node information or lose the connection of the original graph; therefore, it is difficult to identify continuous subtructures. Importantly, they lacked interpretability on molecular graphs. To this end, we proposed a novel Molecular Edge Shrinkage Pooling (MESPool) method, which is based on edges (or chemical bonds). MESPool preserves crucial edges and shrinks others inside the functional groups and is able to search for key structures without breaking the original connection. We compared MESPool with various well-known pooling methods on different benchmarks and showed that MESPool outperforms the previous methods. Furthermore, we explained the rationality of MESPool on some datasets, including a COVID-19 drug dataset.
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Affiliation(s)
- Fanding Xu
- School of Life Science and Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
| | - Zhiwei Yang
- School of Physics, Xi’an Jiaotong University, 710049 Shaanxi, China
| | - Lizhuo Wang
- School of Life Science and Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
| | - Deyu Meng
- Rearch Institute for Mathematics and Mathematical Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
- School of Mathematics and Statistics, Henan University, 475004 Henan, China
| | - Jiangang Long
- School of Life Science and Technology, Xi’an Jiaotong University, 710049 Shaanxi, China
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2
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Exploring novel functionality for efficient extraction of UO22+ and Th4+in ionic liquid: Mechanism, speciation, selectivity, stability and stripping. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Moussa-Pacha NM, Abdin SM, Omar HA, Alniss H, Al-Tel TH. BACE1 inhibitors: Current status and future directions in treating Alzheimer's disease. Med Res Rev 2019; 40:339-384. [PMID: 31347728 DOI: 10.1002/med.21622] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/22/2019] [Accepted: 06/13/2019] [Indexed: 12/28/2022]
Abstract
Alzheimer's disease (AD) is an irreversible, progressive neurodegenerative brain disorder with no current cure. One of the important therapeutic approaches of AD is the inhibition of β-site APP cleaving enzyme-1 (BACE1), which is involved in the rate-limiting step of the cleavage process of the amyloid precursor protein (APP) leading to the generation of the neurotoxic amyloid β (Aβ) protein after the γ-secretase completes its function. The produced insoluble Aβ aggregates lead to plaques deposition and neurodegeneration. BACE1 is, therefore, one of the attractive targets for the treatment of AD. This approach led to the development of potent BACE1 inhibitors, many of which were advanced to late stages in clinical trials. Nonetheless, the high failure rate of lead drug candidates targeting BACE1 brought to the forefront the need for finding new targets to uncover the mystery behind AD. In this review, we aim to discuss the most promising classes of BACE1 inhibitors with a description and analysis of their pharmacodynamic and pharmacokinetic parameters, with more focus on the lead drug candidates that reached late stages of clinical trials, such as MK8931, AZD-3293, JNJ-54861911, E2609, and CNP520. In addition, the manuscript discusses the safety concerns and insignificant physiological effects, which were highlighted for the most successful BACE1 inhibitors. Furthermore, the review demonstrates with increasing evidence that despite tremendous efforts and promising results conceived with BACE1 inhibitors, the latest studies suggest that their clinical use for treating Alzheimer's disease should be reconsidered. Finally, the review sheds light on alternative therapeutic options for targeting AD.
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Affiliation(s)
- Nour M Moussa-Pacha
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Shifaa M Abdin
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Hasan Alniss
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,College of Pharmacy and College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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Atlam F, Awad M, Salama R. Factors Influencing the Potency of Alzheimer Inhibitors: Computational and Docking Studies. Am J Alzheimers Dis Other Demen 2018; 33:166-175. [PMID: 29301410 PMCID: PMC10852456 DOI: 10.1177/1533317517749207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Density functional theory (B3LYP/6-31G [d]) is performed to study the effect of molecular and electronic structures of the investigated β-secretase 1 (BACE1) Alzheimer's inhibitors on their biological activities and discuss the correlation between their inhibition efficiencies and quantum chemical descriptors. IC50 values of the investigated compounds are mostly affected by the substituted R2 phenyl moiety. The calculations show that the presence of electron withdrawing group increases the half maximal inhibitory concentration (IC50). Structure-activity relationship studies show that the electronic descriptors, energy of high occupied molecular orbital, ΔE, lipophilicity, hardness, and ionization potential index, are the most significant descriptors for the correlation with IC50. Molecular docking simulation is performed to explain the mode of interaction between the most potent drug and the binding sites of the BACE1 target. A good correlation between the experimental and the theoretical data confirms that the quantum chemical methods are successful tools for the discovery of novel BACE1 drugs.
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Affiliation(s)
- Faten Atlam
- Theoretical applied Chemistry Unit (TACU), Chemistry Department, Tanta University, Tanta, Egypt
| | - Mohamed Awad
- Theoretical applied Chemistry Unit (TACU), Chemistry Department, Tanta University, Tanta, Egypt
| | - Rehab Salama
- Theoretical applied Chemistry Unit (TACU), Chemistry Department, Tanta University, Tanta, Egypt
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Ghanbarimasir Z, Bekhradnia A, Morteza-Semnani K, Rafiei A, Razzaghi-Asl N, Kardan M. Design, synthesis, biological assessment and molecular docking studies of new 2-aminoimidazole-quinoxaline hybrids as potential anticancer agents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 194:21-35. [PMID: 29310028 DOI: 10.1016/j.saa.2017.12.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/17/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
In a search for novel antiproliferative agents, a series of quinoxaline derivatives containing 2-aminoimidazole (8a-8x) were designed and synthesized. The structures of synthesized compounds were confirmed by IR, 1H NMR, 13C NMR, Mass Spectroscopy and analyzed using HSQC, COSY, ROESY, HMBC techniques. The anticancer activity of all derivatives were evaluated for colon cancer and breast cancer cell lines by the MTT assay and acridine orange/ethidium bromide double staining method. The anti-cancer effect in human colon cancer (HCT-116) and breast cancer (MCF-7) cell lines exhibited that compounds 8a, 8s, 8t, 8w, 8x appeared as potent antiproliferative agents and especially inhibited the human colon cancer cell proliferation with percentage of inhibition by over 50%. The most active compound was (E)-4-phenyl-1-((quinoxalin-2-ylmethylene)amino)-1H-imidazol-2-amine (8a) with the highest inhibition for MCF-7 (83.3%) and HCT-116 (70%) cell lines after 48 and 24h, respectively. Molecular docking studies of these derivatives within c-kit active site as a validated target might be suggested them as appropriate candidates for further efforts toward more potent anticancer compounds.
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Affiliation(s)
- Zahra Ghanbarimasir
- Student Research Committee, Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ahmadreza Bekhradnia
- Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Katayoun Morteza-Semnani
- Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Mazandaran University of Medical Sciences, Sari, Iran
| | - Alireza Rafiei
- Molecular and Cell Biology Research Center, Hemoglobinopathy Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mostafa Kardan
- Molecular and Cell Biology Research Center, Hemoglobinopathy Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Kumar A, Srivastava G, Srivastava S, Verma S, Negi AS, Sharma A. Investigation of naphthofuran moiety as potential dual inhibitor against BACE-1 and GSK-3β: molecular dynamics simulations, binding energy, and network analysis to identify first-in-class dual inhibitors against Alzheimer's disease. J Mol Model 2017; 23:239. [PMID: 28741112 DOI: 10.1007/s00894-017-3396-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 12/11/2022]
Abstract
BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches. Docking study of naphthofuran series showed a good binding affinity towards both the targets. Molecular dynamics, binding energy, and network analysis were performed to compare their binding with the targets and amino acids responsible for binding. Naphthofuran series derivatives showed good interaction within the active site residues of both of the targets. Hydrogen bond occupancy and binding energy suggested strong binding with the targets. Dual-inhibitor binding was mostly governed by the hydrophobic interactions for both of the targets. Per residue energy decomposition and network analysis identified the key residues involved in the binding and inhibiting BACE-1 and GSK-3β. The results indicated that naphthofuran series derivative 11 may be a promising first-in-class dual inhibitor against BACE-1 and GSK-3β. This naphthofuran series may be further explored to design better dual inhibitors. Graphical abstract Naphthofuran derivative as a dual inhibitor for BACE-1 and GSK-3β.
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Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Swati Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Seema Verma
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Arvind S Negi
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India.
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RAZZAGHI-ASL NIMA, SHAHABIPOUR SARA, EBADI AHMAD, BAGHERI AZAM. Quantum chemical analysis of potential anti-Parkinson agents. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0889-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Silva T, Borges F, Edraki N, Alizadeh M, Miri R, Saso L, Firuzi O. Hydroxycinnamic acid as a novel scaffold for the development of cyclooxygenase-2 inhibitors. RSC Adv 2015. [DOI: 10.1039/c5ra08692b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The most active hydroxycinnamic acid derivative, caffeic acid diethyl ester (CA-DE), demonstrated 88.5/30.5% inhibition at 100/20 μM against COX-2 and negligible COX-1 inhibitory effect. CA-DE showed preferred interactions with COX-2 active site.
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Affiliation(s)
- T. Silva
- CIQ/Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
- Portugal
| | - F. Borges
- CIQ/Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
- Portugal
| | - N. Edraki
- Medicinal and Natural Products Chemistry Research Center
- Shiraz University of Medical Sciences
- Shiraz
- Iran
| | - M. Alizadeh
- Medicinal and Natural Products Chemistry Research Center
- Shiraz University of Medical Sciences
- Shiraz
- Iran
| | - R. Miri
- Medicinal and Natural Products Chemistry Research Center
- Shiraz University of Medical Sciences
- Shiraz
- Iran
| | - L. Saso
- Department of Physiology and Pharmacology Vittorio Erspamer
- Sapienza University of Rome
- Rome
- Italy
| | - O. Firuzi
- Medicinal and Natural Products Chemistry Research Center
- Shiraz University of Medical Sciences
- Shiraz
- Iran
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Molecular docking and quantum mechanical studies on biflavonoid structures as BACE-1 inhibitors. Struct Chem 2014. [DOI: 10.1007/s11224-014-0523-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Design and synthesis of novel 3,5-bis-N-(aryl/heteroaryl) carbamoyl-4-aryl-1,4-dihydropyridines as small molecule BACE-1 inhibitors. Bioorg Med Chem 2013; 21:6893-909. [DOI: 10.1016/j.bmc.2013.09.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/04/2013] [Accepted: 09/12/2013] [Indexed: 11/23/2022]
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11
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Ebadi A, Razzaghi-Asl N, Khoshneviszadeh M, Miri R. Comparative amino acid decomposition analysis of potent type I p38α inhibitors. ACTA ACUST UNITED AC 2013; 21:41. [PMID: 23714278 PMCID: PMC3680208 DOI: 10.1186/2008-2231-21-41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 05/25/2013] [Indexed: 12/21/2022]
Abstract
Background and purpose of the study p38α is a member of mitogen-activated protein kinases (MAPK) considered as a prominent target in development of anti-inflammatory agents. Any abnormality in the phosphorylation process leads to the different human diseases such as cancer, diabetes and inflammatory diseases. Several small molecule p38α inhibitors have been developed up to now. In this regard, structural elucidation of p38 inhibitors needs to be done enabling us in rational lead development strategies. Methods Various interactions of three potent inhibitors with p38α active site have been evaluated in terms of binding energies and bond lengths via density function theory and MD simulations. Results Our comparative study showed that both ab initio and MD simulation led to the relatively similar results in pharmacophore discrimination of p38α inhibitors. Conclusion The results of the present study may find their usefulness in pharmacophore based modification of p38α inhibitors.
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Affiliation(s)
- Ahmad Ebadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, PO Box 3288-71345, Shiraz, Iran.
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