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Qiu Y, Wang Y, Lu J, Zhu Q, Jia L, Lei F, Shen L, Jiang L, Wu A. Synthesis, spectroscopic analysis, DFT, docking, MD and antioxidant activity of tetrahydrocurcumin. J Biomol Struct Dyn 2023:1-13. [PMID: 37902569 DOI: 10.1080/07391102.2023.2275189] [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: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023]
Abstract
In recent years, numerous researchers have made local chemical modifications to the structure of curcumin while its basic structure remains unchanged, thus, producing curcumin derivatives. In this article, tetrahydrocurcumin was obtained by hydrogenation of curcumin, DFT calculation and characterization at the theoretical level of B3LYP/6 -311++G(d,p) were carried out. The observed IR and Raman spectra are in good agreement with the theoretical spectra. The FMO and ESP of tetrahydrocurcumin are predicted. The interaction in the system is shown graphically and analyzed by IGMH. Compared with curcumin, tetrahydrocurcumin lacks the unsaturated C = C bond, which makes it more stable and more bioavailable. Molecular docking with antioxidant targets elucidated the ligand-protein interaction and molecular dynamics simulation showed the antioxidant activity of tetrahydrocurcumin. The antioxidant activity of tetrahydrocurcumin was proved by DPPH• and •OH radical scavenging experiments. In essence, these derivatives exhibit enhanced physiological activity in certain aspects compared to the original curcumin. Moreover, the computational pharmacology techniques lay a theoretical groundwork for the development and modification of high-efficiency, low-toxicity drugs that interface with various targets of curcumin in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yingqi Qiu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Yuanmeng Wang
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Jiahao Lu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Qinghua Zhu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Li Jia
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Fuhou Lei
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Liqun Shen
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Lihe Jiang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
- Medical College, Guangxi University, Nanning, China
| | - Aiqun Wu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
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El Aissouq A, Bouachrine M, Bouayyadi L, Ouammou A, Khalil F. Structure-based virtual screening of novel natural products as chalcone derivatives against SARS-CoV-2 M pro. J Biomol Struct Dyn 2023; 41:13235-13249. [PMID: 36752320 DOI: 10.1080/07391102.2023.2172456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from spreading, but there are currently no approved medicines to treat COVID-19. In this work, a dataset of 142 natural products collected from various medicinal plants was used to perform structure-based virtual screening (SBVS) through the combined application of molecular docking and molecular dynamics (MD) simulation methods. First, the dataset of compounds was optimized using the density functional theory (DFT) approach. The optimized compounds were then submitted to the first screening, which was done by the pKCM web server to look for drug-likeness and the PyRx to look for binding affinity. Among the 142 natural substances, 10 compounds were selected for docking validation. Compounds that interact with CYS145 and LEU141, the essential catalytic residues, as well as compounds with binding affinities less than -8.0 kcal/mol, are considered promising anti-SARS-CoV-2 drug candidates. The top-ranked compounds were then evaluated by MD simulations and MM-GBSA method. These results could help researchers come up with new natural compounds that could be used to treat SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdellah El Aissouq
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Bouachrine
- MCNS Laboratory, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | | | - Abdelkrim Ouammou
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Fouad Khalil
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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Yu CX, Tan JW, Rullah K, Imran S, Tham CL. Insight parameter drug design for human β-tryptase inhibition integrated molecular docking, QSAR, molecular dynamics simulation, and pharmacophore modelling studies of α-keto-[1,2,4]-oxadiazoles. J Biomol Struct Dyn 2023; 41:12978-12996. [PMID: 36709457 DOI: 10.1080/07391102.2023.2171131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/11/2023] [Indexed: 01/30/2023]
Abstract
Dengue hemorrhagic fever (DHF) is severe dengue with a hallmark of vascular leakage. β-tryptase has been found to promote vascular leakage in DHF patients, which could be a potential target for DHF treatment. This study aims to develop a theoretical background for designing and selecting human β-tryptase inhibitors through computational studies. Thirty-four α-keto-[1,2,3]-oxadiazoles scaffold-based compounds were used to generate 2D-QSAR models and for molecular docking studies with β-tryptase (PDB Code 4A6L). In addition, molecular dynamics (MD) simulation and molecular mechanics generalised born surface area (MM-GBSA) analysis on the binding of the reported most active compound, compound 11e, towards β-tryptase were performed. Finally, a structure-based pharmacophore model was generated. The selected 2D-QSAR models have statistically proven good models by internal and external validation as well as the y-randomization test. The docking results of compound 11e showed lower CDOCKER energy than the 4A6L co-crystallised ligand and a similar binding pattern as the 4A6L co-crystallised ligand. From molecular dynamics simulation, 4A6L in compound 11e bound state has RMSD below 2 Å throughout the 500 ns simulation, indicating the docked complex is stable. Besides, MM-GBSA analysis suggested the 4A6L-compound 11e docked complex (-66.04 Kcal/mol) is structurally as stable as the 4A6L-native ligand co-crystallized structure (-66.84 Kcal/mol). The best pharmacophore model identified features included hydrogen bond acceptor, ionic interaction, hydrophobic interaction, and aromatic ring, which contribute to the inhibitory potency of a compound. This study supplied insight and knowledge for developing novel chemical compounds with improved inhibition of β-tryptase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chai Xin Yu
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Jian Wei Tan
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Kamal Rullah
- Drug Discovery and Synthetic Chemistry Research Group, Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Science, Universiti Teknologi MARA (UiTM), Shah Alam, Selangor, Malaysia
| | - Chau Ling Tham
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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El Aissouq A, Bouachrine M, Ouammou A, Khalil F. Homology modeling, virtual screening, molecular docking, molecular dynamic (MD) simulation, and ADMET approaches for identification of natural anti-Parkinson agents targeting MAO-B protein. Neurosci Lett 2022; 786:136803. [PMID: 35842207 DOI: 10.1016/j.neulet.2022.136803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/30/2022]
Abstract
Monoamine oxidase-B (MAO-B) is a flavin-dependent enzyme involved in various neurodegenerative disorders. Here, a dataset of 142 chalcone derivatives, collected from various natural plants, was screened by combining structure-based virtual screening and ADMET approaches. The goal is to discover novel natural chalcones as potential MAO-B inhibitors. With the help of the Gaussian 09.5 software, the 3D chemical structures of compounds were optimized using the DFT method. The 3D structure of the hMAO-B enzyme was built using the Modeller software. The optimized structures were subjected to virtual screening by Autodock Vina, implicated in PyRx software. Among the 142 natural substances, 43 were selected based on their binding affinity. Then, the pharmacokinetic proprieties and toxicity of these compounds were evaluated using ADMET analysis. Ten compounds were predicted to have ADMET characteristics with no side effects. The binding modes and interactions of the top selected compounds were then evaluated using AutoDock 4.2. Compounds P60 and P81 were found to be potential inhibitors of MAO-B compared to rasagiline, safinamid, and selegiline, the reference drugs. The stability of the selected compounds was confirmed by MD simulation. Based on this finding, compounds P60 and P81 could be considered potential hMAO-B inhibitors.
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Affiliation(s)
- Abdellah El Aissouq
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco.
| | - Mohammed Bouachrine
- MCNS Laboratory, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Abdelkrim Ouammou
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Fouad Khalil
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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El Aissouq A, Chedadi O, Bouachrine M, Ouammou A, Khalil F. Development of novel monoamine oxidase B (MAO-B) inhibitors by combined application of docking-based alignment, 3D-QSAR, ADMET prediction, molecular dynamics simulation, and MM_GBSA binding free energy. J Biomol Struct Dyn 2022:1-14. [PMID: 35510607 DOI: 10.1080/07391102.2022.2071341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Unsaturated ketone derivatives are known as inhibitors of monoamine oxidase B (MAO-B), a potential drug target of Parkinson's disease. Here, docking-based alignment, 3 D-QSAR (three-dimensional quantitative structure-activity relationship) studies, ADMET (absorption, distribution, metabolism, excretion, and toxicity) prediction, molecular dynamics (MD) simulation, and MM_GBSA binding free energy were performed on a novel series of MAO-B inhibitors. The objective is to predict new MAO-B inhibitors with high potency activity. The 3 D-QSAR models were created using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA). Molecular docking findings indicated that compounds with strong inhibitory efficacy also had a high binding affinity. 3 D-QSAR studies showed the importance of steric, electrostatic, and H-bond acceptor fields on the inhibitory activity of MAO-B. Based on the appropriate 3 D-QSAR model, a new series of MAO-B inhibitors were predicted and their pharmacokinetic characteristics were evaluated using in silico ADMET prediction. All screened compounds show good oral bioavailability without any side effects. Moreover, the dynamic behavior and stability of the most active compounds were evaluated using MD simulations. The results showed that unsaturated ketone derivatives are stable and compact during the 100 ns of MD simulation. Finally, the binding free energy of complexes was determined using the MM_GBSA method; the findings indicated that the T1 compound is more stable (ΔGbinding = -409.506 KJ/mol) than the data set's highest active compound (ΔGbinding = -31.883 KJ/mol).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdellah El Aissouq
- LPME Laboratory, Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Oussama Chedadi
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Bouachrine
- MCNS Laboratory, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Abdelkrim Ouammou
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Fouad Khalil
- LPME Laboratory, Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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El Aissouq A, Lachhab A, El Rhabori S, Bouachrine M, Ouammou A, Khalil F. Computer-aided drug design applied to a series of pyridinyl imidazole derivatives targeting p38α MAP kinase: 2D-QSAR, docking, MD simulation, and ADMET investigations. NEW J CHEM 2022. [DOI: 10.1039/d2nj03686j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The p38 mitogen-activated protein kinase (MAPK) is a crucial target for chronic inflammation.
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Affiliation(s)
- Abdellah El Aissouq
- Laboratory of Processes, Materials and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Aissam Lachhab
- Laboratory of Processes, Materials and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Said El Rhabori
- Laboratory of Processes, Materials and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Bouachrine
- MCNS Laboratory, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Abdelkrim Ouammou
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Fouad Khalil
- Laboratory of Processes, Materials and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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