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Liao Y, Cao P, Luo L. Development of novel ALOX15 inhibitors combining dual machine learning filtering and fragment substitution optimisation approaches, molecular docking and dynamic simulation methods. J Enzyme Inhib Med Chem 2024; 39:2301756. [PMID: 38213304 PMCID: PMC10791093 DOI: 10.1080/14756366.2024.2301756] [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: 06/09/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024] Open
Abstract
The oxidation of unsaturated lipids, facilitated by the enzyme Arachidonic acid 15-lipoxygenase (ALOX15), is an essential element in the development of ferroptosis. This study combined a dual-score exclusion strategy with high-throughput virtual screening, naive Bayesian and recursive partitioning machine learning models, the already established ALOX15 inhibitor i472, and a docking-based fragment substitution optimisation approach to identify potential ALOX15 inhibitors, ultimately leading to the discovery of three FDA-approved drugs that demonstrate optimal inhibitory potential against ALOX15. Through fragment substitution-based optimisation, seven new inhibitor structures have been developed. To evaluate their practicality, ADMET predictions and molecular dynamics simulations were performed. In conclusion, the compounds found in this study provide a novel approach to combat conditions related to ferroptosis-related injury by inhibiting ALOX15.
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Affiliation(s)
- Yinglin Liao
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Peng Cao
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
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Zhuravlev A, Cruz A, Aksenov V, Golovanov A, Lluch JM, Kuhn H, González-Lafont À, Ivanov I. Different Structures-Similar Effect: Do Substituted 5-(4-Methoxyphenyl)-1 H-indoles and 5-(4-Methoxyphenyl)-1 H-imidazoles Represent a Common Pharmacophore for Substrate Selective Inhibition of Linoleate Oxygenase Activity of ALOX15? Molecules 2023; 28:5418. [PMID: 37513289 PMCID: PMC10383952 DOI: 10.3390/molecules28145418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Mammalian 15-lipoxygenases (ALOX15) are lipid peroxidizing enzymes that exhibit variable functionality in different cancer and inflammation models. The pathophysiological role of linoleic acid- and arachidonic acid-derived ALOX15 metabolites rendered this enzyme a target for pharmacological research. Several indole and imidazole derivatives inhibit the catalytic activity of rabbit ALOX15 in a substrate-specific manner, but the molecular basis for this allosteric inhibition remains unclear. Here, we attempt to define a common pharmacophore, which is critical for this allosteric inhibition. We found that substituted imidazoles induce weaker inhibitory effects when compared with the indole derivatives. In silico docking studies and molecular dynamics simulations using a dimeric allosteric enzyme model, in which the inhibitor occupies the substrate-binding pocket of one monomer, whereas the substrate fatty acid is bound at the catalytic center of another monomer within the ALOX15 dimer, indicated that chemical modification of the core pharmacophore alters the enzyme-inhibitor interactions, inducing a reduced inhibitory potency. In our dimeric ALOX15 model, the structural differences induced by inhibitor binding are translated to the hydrophobic dimerization cluster and affect the structures of enzyme-substrate complexes. These data are of particular importance since substrate-specific inhibition may contribute to elucidation of the putative roles of ALOX15 metabolites derived from different polyunsaturated fatty acids in mammalian pathophysiology.
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Affiliation(s)
- Alexander Zhuravlev
- Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia
| | - Alejandro Cruz
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Vladislav Aksenov
- Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklihio-Maklaja Str., 16/10c4, 117997 Moscow, Russia
| | - Alexey Golovanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Hartmut Kuhn
- Department of Biochemistry, Charite-University Medicine Berlin, Corporate Member of Free University Berlin and Humboldt University Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Igor Ivanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia
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Liao Y, Cao P, Luo L. Identification of Novel Arachidonic Acid 15-Lipoxygenase Inhibitors Based on the Bayesian Classifier Model and Computer-Aided High-Throughput Virtual Screening. Pharmaceuticals (Basel) 2022; 15:1440. [PMID: 36422570 PMCID: PMC9695033 DOI: 10.3390/ph15111440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 08/29/2023] Open
Abstract
Ferroptosis is an iron-dependent lipid peroxidative form of cell death that is distinct from apoptosis and necrosis. ALOX15, also known as arachidonic acid 15-lipoxygenase, promotes ferroptosis by converting intracellular unsaturated lipids into oxidized lipid intermediates and is an important ferroptosis target. In this study, a naive Bayesian machine learning classifier with a structure-based, high-throughput screening approach and a molecular docking program were combined to screen for three compounds with excellent target-binding potential. In the absorption, distribution, metabolism, excretion, and toxicity characterization, three candidate molecules were predicted to exhibit drug-like properties. The subsequent molecular dynamics simulations confirmed their stable binding to the targets. The findings indicated that the compounds exhibited excellent potential ALOX15 inhibitor capacity, thereby providing novel candidates for the treatment of inflammatory ischemia-related diseases caused by ferroptosis.
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Affiliation(s)
- Yinglin Liao
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China
| | - Peng Cao
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
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Benatzy Y, Palmer MA, Brüne B. Arachidonate 15-lipoxygenase type B: Regulation, function, and its role in pathophysiology. Front Pharmacol 2022; 13:1042420. [PMID: 36438817 PMCID: PMC9682198 DOI: 10.3389/fphar.2022.1042420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 10/30/2023] Open
Abstract
As a lipoxygenase (LOX), arachidonate 15-lipoxygenase type B (ALOX15B) peroxidizes polyenoic fatty acids (PUFAs) including arachidonic acid (AA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and linoleic acid (LA) to their corresponding fatty acid hydroperoxides. Distinctive to ALOX15B, fatty acid oxygenation occurs with positional specificity, catalyzed by the non-heme iron containing active site, and in addition to free PUFAs, membrane-esterified fatty acids serve as substrates for ALOX15B. Like other LOX enzymes, ALOX15B is linked to the formation of specialized pro-resolving lipid mediators (SPMs), and altered expression is apparent in various inflammatory diseases such as asthma, psoriasis, and atherosclerosis. In primary human macrophages, ALOX15B expression is associated with cellular cholesterol homeostasis and is induced by hypoxia. Like in inflammation, the role of ALOX15B in cancer is inconclusive. In prostate and breast carcinomas, ALOX15B is attributed a tumor-suppressive role, whereas in colorectal cancer, ALOX15B expression is associated with a poorer prognosis. As the biological function of ALOX15B remains an open question, this review aims to provide a comprehensive overview of the current state of research related to ALOX15B.
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Affiliation(s)
- Yvonne Benatzy
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt, Germany
| | - Megan A. Palmer
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt, Germany
| | - Bernhard Brüne
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
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Golovanov A, Zhuravlev A, Cruz A, Aksenov V, Shafiullina R, Kakularam KR, Lluch JM, Kuhn H, González-Lafont À, Ivanov I. N-Substituted 5-(1H-Indol-2-yl)-2-methoxyanilines Are Allosteric Inhibitors of the Linoleate Oxygenase Activity of Selected Mammalian ALOX15 Orthologs: Mechanism of Action. J Med Chem 2022; 65:1979-1995. [DOI: 10.1021/acs.jmedchem.1c01563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alexey Golovanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA─Russian Technological University, Vernadskogo Pr. 86, 119571 Moscow, Russia
| | - Alexander Zhuravlev
- Lomonosov Institute of Fine Chemical Technologies, MIREA─Russian Technological University, Vernadskogo Pr. 86, 119571 Moscow, Russia
| | - Alejandro Cruz
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Vladislav Aksenov
- Lomonosov Institute of Fine Chemical Technologies, MIREA─Russian Technological University, Vernadskogo Pr. 86, 119571 Moscow, Russia
| | - Rania Shafiullina
- Lomonosov Institute of Fine Chemical Technologies, MIREA─Russian Technological University, Vernadskogo Pr. 86, 119571 Moscow, Russia
| | - Kumar R. Kakularam
- Department of Biochemistry, Charite─University Medicine Berlin, Corporate Member of Free University Berlin, Humboldt University Berlin and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - José M. Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Hartmut Kuhn
- Department of Biochemistry, Charite─University Medicine Berlin, Corporate Member of Free University Berlin, Humboldt University Berlin and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Igor Ivanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA─Russian Technological University, Vernadskogo Pr. 86, 119571 Moscow, Russia
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