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Guevara-Martínez SJ, Villanueva-Mejía F, Zamudio-Ojeda A, Herrera-Bucio R, Morales-Palacios FG. Isolation of the Antifungal Compound Alliodorin from the Heartwood of Cordia elaeagnoides A. DC. and the In Silico Analysis of the Laccase. PLANTS (BASEL, SWITZERLAND) 2024; 13:1294. [PMID: 38794364 PMCID: PMC11125024 DOI: 10.3390/plants13101294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024]
Abstract
Cordia elaeagnoides A. DC. is an endemic species of Mexico valued for its timber. Renowned for its durability, resistance, and versatile applications in medicine, this tree holds significant commercial importance. Tetrahydrofuran (THF) extract from the heartwood of C. elaeagnoides was studied. Through chromatographic column purification, the compound 8-(2,5-Dihydroxyphenyl)-2,6-dimethylocta-2,6-dienal, also known as alliodorin, was successfully isolated. Identification of alliodorin was confirmed through comprehensive analysis utilizing NMR, IR, and mass spectrometry techniques. Inhibition tests were conducted using both the THF extract and alliodorin against the rotting fungus Trametes versicolor (L.) Lloyd, employing the agar well diffusion assay. Remarkably, alliodorin exhibited 100% inhibition with a median lethal concentration of 0.079 mg/mL and a total lethal concentration of 0.127 mg/mL, in comparison to the commercial fungicide benomyl, which requires a concentration of 1 mg/mL. In silico analysis through molecular docking on the laccase enzyme was proposed in order to explain the inhibitory activity against the fungus T. versicolor, as this enzyme is one of the main sources of nutrients and development for the fungus. Based on these findings, we deduced that alliodorin holds promise as a potent antifungal agent, potentially applicable in a wide array of technological and environmentally friendly initiatives.
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Affiliation(s)
- Santiago José Guevara-Martínez
- Department of Pharmacology, School of Exact Sciences and Engineering, University of Guadalajara, Boulevard Gral. Marcelino García Barragán 1421, Olímpica, Guadalajara 44840, Jalisco, Mexico;
| | - Francisco Villanueva-Mejía
- Instituto Tecnológico de Pabellón de Arteaga, Carretera a la estación de Rincón de Romos, km 1, Aguacalientes 20670, Aguascalientes, Mexico;
| | - Adalberto Zamudio-Ojeda
- Deparment of Physics, School of Exact Sciences and Engineering, University of Guadalajara, Boulevard Gral. Marcelino García Barragán 1421, Olímpica, Guadalajara 44840, Jalisco, Mexico;
| | - Rafael Herrera-Bucio
- Instituto de Investigaciones Químico Biólogicas, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica, s/n, Morelia 58030, Michoacán, Mexico
| | - Fredy Geovannini Morales-Palacios
- Instituto de Investigaciones Químico Biólogicas, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica, s/n, Morelia 58030, Michoacán, Mexico
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Chen Z, Shi Q, Zhao T, Liu Y, Hao J, Li Z, Ning L. Molecular insights into inhibiting effects of lignin on cellulase investigated by molecular dynamics simulation. J Biomol Struct Dyn 2024:1-13. [PMID: 38497800 DOI: 10.1080/07391102.2024.2328738] [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: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024]
Abstract
The hydrolysis of lignocellulose into fermentable monosaccharides using cellulases represents a critical stage in lignocellulosic bioconversion. However, the inactivation of cellulase in the presence of lignin is attributed to the high cost of biofinery. To address this challenge, a comprehensive investigation into the structure-function relationship underlying lignin-driven cellulase inactivation is essential. In this study, molecular docking and molecular dynamics (MD) simulations were employed to explore the impacts of lignin fragments on the catalytic efficiency of cellulase at the atomic level. The findings revealed that soluble lignin fragments and cellulose could spontaneously form stable complexes with cellulase, indicating a competitive binding scenario. The enzyme's structure remained unchanged upon binding to lignin. Furthermore, specific amino acid residues have been identified as involved in interactions with lignin and cellulose. Hydrophobic interactions were found to dominate the binding of lignin to cellulase. Based on the mechanisms underlying the interactions between lignin fragments and cellulase, decreased hydrophobicity and change in the charge of lignin may mitigate the inhibition of cellulase. Furthermore, site mutations and chemical modification are also feasible to improve the efficiency of cellulase. This study may contribute valuable insights into the design of more lignin-resistant enzymes and the optimization of lignocellulosic pretreatment technologies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhenjuan Chen
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Qingwen Shi
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Tengfei Zhao
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Yuxi Liu
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Jinhong Hao
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Zhijian Li
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
| | - Lulu Ning
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, P. R. China
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Cárdenas-Moreno Y, González-Bacerio J, García Arellano H, Del Monte-Martínez A. Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst. Biotechnol Appl Biochem 2023; 70:2108-2135. [PMID: 37753743 DOI: 10.1002/bab.2513] [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: 09/26/2022] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.
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Affiliation(s)
- Yosberto Cárdenas-Moreno
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jorge González-Bacerio
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, Havana, Cuba
| | - Humberto García Arellano
- Department of Environmental Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University, Lerma, Mexico, Mexico
| | - Alberto Del Monte-Martínez
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
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Silva MA, Nascimento Júnior JCD, Thomaz DV, Maia RT, Costa Amador V, Tommaso G, Coelho GD. Comparative homology of Pleurotus ostreatus laccase enzyme: Swiss model or Modeller? J Biomol Struct Dyn 2023; 41:8927-8940. [PMID: 36310115 DOI: 10.1080/07391102.2022.2138975] [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: 07/15/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
Laccases stand out in the industrial context due to their versatile biotechnological applications. Although these enzymes are frequently investigated, currently, Pleurotus ostreatus laccase structural model is unknown. Therefore, this research aims to predict and validate a P. ostreatus laccase theoretical model by means of comparative homology. The laccase target's primary structure (AOM73725.1) was obtained from the NCBI database, the model was predicted from homologous structures obtained from the PDB (PDB-ID: 5A7E, 2HRG, 4JHU, 1GYC) using the Swiss-Model and Modeller, and was refined in GalaxyRefine. The models were validated using PROCHECK, VERIFY 3D, ERRAT, PROVE and QMEAN Z-score servers. Moreover, molecular docking between the laccase model (Lacc4MN) and ABTS was performed on AutoDock Vina. The models that were generated by the Modeller showed superior stereochemical and structural characteristics to those predicted by the Swiss Model. The refinement made it difficult to stabilize the copper atoms which are typical of laccases. The Lacc4MN model showed the interactions between the amino acids in the active site of the laccase and the copper atoms, thereby hinting the stabilization of the metal through electrostatic interactions with histidine and cysteine. The molecular docking between Lacc4MN and ABTS showed negative free energy and the formation of two hydrogen bonds involving the amino acids ASP 208 and GLY 268, and a Pi-sulfur bond between residue HIS 458 and ABTS, which demonstrates the typical catalytic functionality of laccases. Furthermore, the theoretical model Lacc4MN presented stereochemical and structural characteristics that allow its use in silico tests.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Marco Antonio Silva
- Laboratory of Environmental Biotechnology, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - José Cordeiro do Nascimento Júnior
- Center for Water Resources and Environmental Studies, São Carlos School of Engineering, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Douglas Vieira Thomaz
- National Enterprise for nanoScience and nanoTechnology (NEST), Istituto Nanoscienze-CNR and Scuola Normale Superiore, Pisa, Italy
| | - Rafael Trindade Maia
- Academic Unit of Rural Education; Center for Sustainable Development of the Semi-Arid, Federal University of Campina Grande, Sumé, Paraiba, Brazil
| | - Vinícius Costa Amador
- Bioscience Center, Genetics Department, Federal University of Pernambuco, Recife, Brazil
| | - Giovana Tommaso
- Laboratory of Environmental Biotechnology, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Glauciane Danusa Coelho
- Academic Unit of Biotechnology Engineering; Center for Sustainable Development of the Semi-Arid, Federal University of Campina Grande, Sumé, Paraiba, Brazil
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Singh AK, Iqbal HMN, Cardullo N, Muccilli V, Fern'andez-Lucas J, Schmidt JE, Jesionowski T, Bilal M. Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology-A review. Int J Biol Macromol 2023:124968. [PMID: 37217044 DOI: 10.1016/j.ijbiomac.2023.124968] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/22/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational frameworks, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Jesús Fern'andez-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanizaci'on El Bosque, 28670 Villaviciosa de Od'on, Spain; Grupo de Investigaci'on en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002 Barranquilla, Colombia
| | - Jens Ejbye Schmidt
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Odense, Denmark
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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Bhatt P, Bhatt K, Chen WJ, Huang Y, Xiao Y, Wu S, Lei Q, Zhong J, Zhu X, Chen S. Bioremediation potential of laccase for catalysis of glyphosate, isoproturon, lignin, and parathion: Molecular docking, dynamics, and simulation. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130319. [PMID: 36356521 DOI: 10.1016/j.jhazmat.2022.130319] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/21/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
The present study aimed to investigate the catalytic degradation produced by laccase in the detoxification of glyphosate, isoproturon, lignin polymer, and parathion. We explored laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion using molecular docking (MD) and molecular dynamics simulation (MDS) approaches. The results suggest that laccase interacts well with glyphosate, lignin polymer, isoproturon, and parathion during biodegradation. We calculated the root mean square deviations (RMSD) of laccase-glyphosate, laccase-lignin polymer, laccase-isoproturon, and laccase-parathion as 0.24 ± 0.02, 0.59 ± 0.32, 0.43 ± 0.07, and 0.43 ± 0.06 nm, respectively. In an aqueous solution, the stability of laccase with glyphosate, lignin polymer, isoproturon, and parathion is mediated through the formation of hydrophobic interactions, hydrogen bonds, and van der Waals interactions. The presence of xenobiotic toxic compounds in the active site changed the conformation of laccase. MDS of the laccase-substrate complexes confirmed their stability during catalytic degradation. Laccase assay results confirmed that the degradation of syringol, dihydroconiferyl alcohol, guaiacol, parathion, isoproturon, and glyphosate were 100%, 99.31%, 95.69%, 60.96%, 54.51%, and 48.34% within 2 h, respectively. Taken together, we describe a novel method to understand the molecular-level biodegradation of xenobiotic compounds through laccase and its potential application in contaminant removal.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Department of Agricultural & Biological Engineering, Purdue University, West Lafayette 47906, USA
| | - Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette 47906, USA
| | - Wen-Juan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Ying Xiao
- Institute of Chemical Engineering, Guangdong Academy of Sciences, Guangzhou 510665, China
| | - Siyi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Jianfeng Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Xixian Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Singh AK, Bilal M, Jesionowski T, Iqbal HMN. Assessing chemical hazard and unraveling binding affinity of priority pollutants to lignin modifying enzymes for environmental remediation. CHEMOSPHERE 2023; 313:137546. [PMID: 36529171 DOI: 10.1016/j.chemosphere.2022.137546] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/23/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Lignin-modifying enzymes (LMEs) are impactful biocatalysts in environmental remediation applications. However, LMEs-assisted experimental degradation neglects the molecular basis of pollutant degradation. Furthermore, throughout the remediation process, the inherent hazards of environmental pollutants remain untapped for in-depth toxicological endpoints. In this investigation, a predictive toxicological framework and a computational framework adopting LMEs were employed to assess the hazards of Priority Pollutants (PP) and its possible LMEs-assisted catalytic screening. The potential hazardous outcomes of PP were assessed using Quantitative structure-activity relationship (QSARs)-based techniques including Toxtree, ECOSAR, and T.E.S.T. tools. Toxicological findings revealed positive outcomes in a multitude of endpoints for all PP. The PP compound 2,3,7,8-TCDD (dioxin) was found to exhibit the lowest concentration of aquatic toxicity implementing aquatic model systems; LC50 as 0.01, 0.01, 0.04 (mg L-1) for Fish (96 H), Daphnid (48 H), Green algae (96 H) respectively. T.E.S.T. results revealed that chloroform, and 2-chlorophenol both seem to be developmental toxicants. Subsequently, LMEs-assisted docking procedure was employed in predictive mitigation of PP. The docking approach as predicted degradation revealed the far lowest docking energy score for Versatile peroxidase (VP)- 2,3,7,8-TCDD docked complex with a binding energy of -9.2 (kcal mol-1), involved PHE-46, PRO-139, PRO-141, ILE-148, LEU-165, HIS-169, LEU-228, MET-262, and MET-265 as key interacting amino acid residues. Second most ranked but lesser than VP, Lignin peroxidase (LiP)- 2,3,7,8-TCDD docked complex exhibited a rather lower binding affinity score (-8.8 kcal mol-1). Predictive degradation screening employing comparative docking revealed varying binding affinities, portraying that each LMEs member has independent feasibility to bind PP as substrate. Predictive findings endorsed the hazardous nature of associated PP in a multitude of endpoints, which could be attenuated by undertaking LMEs as a predictive approach to protect the environment and implement it in regulatory considerations.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
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Wang X, Kong F, Lin Z. Cromolyn prevents cerebral vasospasm and dementia by targeting WDR43. Front Aging Neurosci 2023; 15:1132733. [PMID: 37122373 PMCID: PMC10133528 DOI: 10.3389/fnagi.2023.1132733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
Background Cerebral vasospasm (CV) can cause inflammation and damage to neuronal cells in the elderly, leading to dementia. Purpose This study aimed to investigate the genetic mechanisms underlying dementia caused by CV in the elderly, identify preventive and therapeutic drugs, and evaluate their efficacy in treating neurodegenerative diseases. Methods Genes associated with subarachnoid hemorrhage and CV were acquired and screened for differentially expressed miRNAs (DEmiRNAs) associated with aneurysm rupture. A regulatory network of DEmiRNAs and mRNAs was constructed, and virtual screening was performed to evaluate possible binding patterns between Food and Drug Administration (FDA)-approved drugs and core proteins. Molecular dynamics simulations were performed on the optimal docked complexes. Optimally docked drugs were evaluated for efficacy in the treatment of neurodegenerative diseases through cellular experiments. Results The study found upregulated genes (including WDR43 and THBS1) and one downregulated gene associated with aneurysm rupture. Differences in the expression of these genes indicate greater disease risk. DEmiRNAs associated with ruptured aortic aneurysm were identified, of which two could bind to THBS1 and WDR43. Cromolyn and lanoxin formed the best docking complexes with WDR43 and THBS1, respectively. Cellular experiments showed that cromolyn improved BV2 cell viability and enhanced Aβ42 uptake, suggesting its potential as a therapeutic agent for inflammation-related disorders. Conclusion The findings suggest that WDR43 and THBS1 are potential targets for preventing and treating CV-induced dementia in the elderly. Cromolyn may have therapeutic value in the treatment of Alzheimer's disease and dementia.
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Hao E, Li Y, Guo B, Yang X, Lu P, Qiao H. Key Residues Affecting Binding Affinity of Sirex noctilio Fabricius Odorant-Binding Protein (SnocOBP9) to Aggregation Pheromone. Int J Mol Sci 2022; 23:ijms23158456. [PMID: 35955589 PMCID: PMC9369295 DOI: 10.3390/ijms23158456] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Sirex noctilio Fabricius (Hymenoptera Siricidae) is a major quarantine pest responsible for substantial economic losses in the pine industry. To achieve better pest control, (Z)-3-decen-ol was identified as the male pheromone and used as a field chemical trapping agent. However, the interactions between odorant-binding proteins (OBPs) and pheromones are poorly described. In this study, SnocOBP9 had a higher binding affinity with Z3D (Ki = 1.53 ± 0.09 μM) than other chemical ligands. Molecular dynamics simulation and binding mode analysis revealed that several nonpolar residues were the main drivers for hydrophobic interactions between SnocOBP9 and Z3D. Additionally, computational alanine scanning results indicated that five amino acids (MET54, PHE57, PHE71, PHE74, LEU116) in SnocOBP9 could potentially alter the binding affinity to Z3D. Finally, we used single-site-directed mutagenesis to substitute these five residues with alanine. These results imply that the five residues play crucial roles in the SnocOBP9-Z3D complex. Our research confirmed the function of SnocOBP9, uncovered the key residues involved in SnocOBP9-Z3D interactions, and provides an inspiration to improve the effects of pheromone agent traps.
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Affiliation(s)
- Enhua Hao
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing 100083, China; (E.H.); (Y.L.); (B.G.); (X.Y.)
| | - Yini Li
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing 100083, China; (E.H.); (Y.L.); (B.G.); (X.Y.)
| | - Bing Guo
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing 100083, China; (E.H.); (Y.L.); (B.G.); (X.Y.)
| | - Xi Yang
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing 100083, China; (E.H.); (Y.L.); (B.G.); (X.Y.)
| | - Pengfei Lu
- Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing 100083, China; (E.H.); (Y.L.); (B.G.); (X.Y.)
- Correspondence: (P.L.); (H.Q.); Tel.: +86-10-6233-6755 (P.L.); +86-10-5783-3180 (H.Q.)
| | - Haili Qiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- Correspondence: (P.L.); (H.Q.); Tel.: +86-10-6233-6755 (P.L.); +86-10-5783-3180 (H.Q.)
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