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Li M, Yang L, Mu C, Sun Y, Gu Y, Chen D, Liu T, Cao H. Gut microbial metabolome in inflammatory bowel disease: From association to therapeutic perspectives. Comput Struct Biotechnol J 2022; 20:2402-2414. [PMID: 35664229 PMCID: PMC9125655 DOI: 10.1016/j.csbj.2022.03.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), is a set of clinically chronic, relapsing gastrointestinal inflammatory disease and lacks of an absolute cure. Although the precise etiology is unknown, developments in high-throughput microbial genomic sequencing significantly illuminate the changes in the intestinal microbial structure and functions in patients with IBD. The application of microbial metabolomics suggests that the microbiota can influence IBD pathogenesis by producing metabolites, which are implicated as crucial mediators of host-microbial crosstalk. This review aims to elaborate the current knowledge of perturbations of the microbiome-metabolome interface in IBD with description of altered composition and metabolite profiles of gut microbiota. We emphasized and elaborated recent findings of several potentially protective metabolite classes in IBD, including fatty acids, amino acids and derivatives and bile acids. This article will facilitate a deeper understanding of the new therapeutic approach for IBD by applying metabolome-based adjunctive treatment.
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Key Words
- AMPs, Antimicrobial peptides
- BAs, Bile acids
- BC, Bray Curtis
- CD, Crohn’s disease
- CDI, Clostridioides difficile infection
- DC, Diversion colitis
- DCA, Deoxycholic acid
- DSS, Dextran sulfate sodium
- FAs, Fatty acid
- FMT, Fecal microbiota transplantation
- FODMAP, Fermentable oligosaccharide, disaccharide, monosaccharide, and polyol
- GC–MS, Gas chromatography-mass spectrometry
- Gut microbiota
- HDAC, Histone deacetylase
- IBD, Inflammatory bowel disease
- Inflammatory bowel diseases
- LC-MS, Liquid chromatography-mass spectrometry
- LCA, Lithocholic acid
- LCFAs, Long-chain fatty acids
- MCFAs, Medium-chain fatty acids
- MD, Mediterranean diet
- MS, Mass spectrometry
- Metabolite
- Metabolomics
- Metagenomics
- Microbial therapeutics
- NMR, Nuclear magnetic resonance
- PBAs, Primary bile acids
- SBAs, Secondary bile acids
- SCD, Special carbohydrate diet
- SCFAs, Short-chain fatty acids
- TNBS, 2,4,6-trinitro-benzene sulfonic acid
- UC, Ulcerative colitis
- UDCA, Ursodeoxycholic acid
- UPLC-MS, ultraperformance liquid chromatography coupled to mass spectrometry
- UU, Unweighted UniFrac
- WMS, Whole-metagenome shotgun
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Affiliation(s)
| | | | | | - Yue Sun
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yu Gu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Danfeng Chen
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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Remya C, Dileep KV, Koti Reddy E, Mantosh K, Lakshmi K, Sarah Jacob R, Sajith AM, Jayadevi Variyar E, Anwar S, Zhang KYJ, Sadasivan C, Omkumar RV. Neuroprotective derivatives of tacrine that target NMDA receptor and acetyl cholinesterase - Design, synthesis and biological evaluation. Comput Struct Biotechnol J 2021; 19:4517-4537. [PMID: 34471497 PMCID: PMC8379669 DOI: 10.1016/j.csbj.2021.07.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
The complex and multifactorial nature of neuropsychiatric diseases demands multi-target drugs that can intervene with various sub-pathologies underlying disease progression. Targeting the impairments in cholinergic and glutamatergic neurotransmissions with small molecules has been suggested as one of the potential disease-modifying approaches for Alzheimer’s disease (AD). Tacrine, a potent inhibitor of acetylcholinesterase (AChE) is the first FDA approved drug for the treatment of AD. Tacrine is also a low affinity antagonist of N-methyl-D-aspartate receptor (NMDAR). However, tacrine was withdrawn from its clinical use later due to its hepatotoxicity. With an aim to develop novel high affinity multi-target directed ligands (MTDLs) against AChE and NMDAR, with reduced hepatotoxicity, we performed in silico structure-based modifications on tacrine, chemical synthesis of the derivatives and in vitro validation of their activities. Nineteen such derivatives showed inhibition with IC50 values in the range of 18.53 ± 2.09 – 184.09 ± 19.23 nM against AChE and 0.27 ± 0.05 – 38.84 ± 9.64 μM against NMDAR. Some of the selected compounds also protected rat primary cortical neurons from glutamate induced excitotoxicity. Two of the tacrine derived MTDLs, 201 and 208 exhibited in vivo efficacy in rats by protecting against behavioral impairment induced by administration of the excitotoxic agent, monosodium glutamate. Additionally, several of these synthesized compounds also exhibited promising inhibitory activitiy against butyrylcholinesterase. MTDL-201 was also devoid of hepatotoxicity in vivo. Given the therapeutic potential of MTDLs in disease-modifying therapy, our studies revealed several promising MTDLs among which 201 appears to be a potential candidate for immediate preclinical evaluations.
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Key Words
- AChE, acetylcholinesterase
- AChEIs, acetylcholinesterase inhibitors
- AChT, acetylthiocholine
- AD, Alzheimer’s disease
- ADME, absorption, distribution, metabolism and excretion
- Acetylcholinesterase
- Alzheimer’s disease
- BBB, blood brain barrier
- Ca2+, calcium
- ChE, Cholinesterases
- DMEM, Dulbecco’s modified Eagle’s medium
- DTNB, 5,5-dithiobis-(2-nitrobenzoic acid)
- ENM, elastic network modeling
- ER, endoplasmic reticulum
- FRET, fluorescence resonance energy transfer
- G6PD, glucose-6-phosphate dehydrogenase
- HBSS, Hank's balanced salt solution
- IP, intraperitoneal
- LBD, Ligand binding domain
- LC-MS, Liquid chromatography-mass spectrometry
- LiCABEDS, Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps
- MAP2, microtubule associated protein 2
- MD, Molecular dynamics
- MTDLs
- MTDLs, multi-target directed ligands
- MWM, Morris water maze
- NBM, neurobasal medium
- NMA, normal mode analysis
- NMDA receptor
- NMDAR, N-methyl-D-aspartate receptor
- Neuroprotection
- OPLS, Optimized potential for liquid simulations
- PBS, phosphate-buffered saline
- PFA, paraformaldehyde
- Polypharmacology
- RMSD, root mean square deviation
- SAR, structure-activity relationships
- SD, standard deviation
- SVM, support vector machine
- Structure-based drug design
- TBI, traumatic brain injury
- TMD, transmembrane domain
- Tacrine
- h-NMDAR, human NMDAR
- hAChE, human AChE
- ppm, parts per million
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Affiliation(s)
- Chandran Remya
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - K V Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Laboratory for Computational and Structural Biology, Jubilee Center for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala 680005, India
| | - Eeda Koti Reddy
- Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Sciences, Technology and Research -VFSTR (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Kumar Mantosh
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Kesavan Lakshmi
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Reena Sarah Jacob
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
| | - Ayyiliyath M Sajith
- Post Graduate and Research Department of Chemistry, Kasargod Govt. College, Kannur University, Kasaragod, India
| | - E Jayadevi Variyar
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - Shaik Anwar
- Division of Chemistry, Department of Sciences and Humanities, Vignan's Foundation for Sciences, Technology and Research -VFSTR (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh 522 213, India
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - C Sadasivan
- Department of Biotechnology and Microbiology, Kannur University, Dr. Janaki Ammal Campus, Thalassery, Kerala 670661, India
| | - R V Omkumar
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala 695014, India
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Picón-Pagès P, Bonet J, García-García J, Garcia-Buendia J, Gutierrez D, Valle J, Gómez-Casuso CE, Sidelkivska V, Alvarez A, Perálvarez-Marín A, Suades A, Fernàndez-Busquets X, Andreu D, Vicente R, Oliva B, Muñoz FJ. Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease. Comput Struct Biotechnol J 2019; 17:963-971. [PMID: 31360335 PMCID: PMC6639691 DOI: 10.1016/j.csbj.2019.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/03/2019] [Accepted: 06/13/2019] [Indexed: 12/01/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative process characterized by the accumulation of extracellular deposits of amyloid β-peptide (Aβ), which induces neuronal death. Monomeric Aβ is not toxic but tends to aggregate into β-sheets that are neurotoxic. Therefore to prevent or delay AD onset and progression one of the main therapeutic approaches would be to impair Aβ assembly into oligomers and fibrils and to promote disaggregation of the preformed aggregate. Albumin is the most abundant protein in the cerebrospinal fluid and it was reported to bind Aβ impeding its aggregation. In a previous work we identified a 35-residue sequence of clusterin, a well-known protein that binds Aβ, that is highly similar to the C-terminus (CTerm) of albumin. In this work, the docking experiments show that the average binding free energy of the CTerm-Aβ1-42 simulations was significantly lower than that of the clusterin-Aβ1-42 binding, highlighting the possibility that the CTerm retains albumin's binding properties. To validate this observation, we performed in vitro structural analysis of soluble and aggregated 1 μM Aβ1-42 incubated with 5 μM CTerm, equimolar to the albumin concentration in the CSF. Reversed-phase chromatography and electron microscopy analysis demonstrated a reduction of Aβ1-42 aggregates when the CTerm was present. Furthermore, we treated a human neuroblastoma cell line with soluble and aggregated Aβ1-42 incubated with CTerm obtaining a significant protection against Aβ-induced neurotoxicity. These in silico and in vitro data suggest that the albumin CTerm is able to impair Aβ aggregation and to promote disassemble of Aβ aggregates protecting neurons.
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Key Words
- AD, Alzheimer's disease
- APP, amyloid precursor protein
- Albumin
- Alzheimer's disease
- Amyloid
- Aß, Amyloid-ß peptide
- CD, Circular dichroism
- CSF, cerebrospinal fluid
- CTerm, albumin C-terminus
- Docking
- HPLC, high performance liquid chromatography
- LC-MS, Liquid chromatography-mass spectrometry
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- NMR, nuclear magnetic resonance
- PBS, phosphate-buffered saline
- PDB, Protein Data Bank
- PPI, protein-protein interactions
- SDS, sodium dodecyl sulfate
- TEM, transmission electron microscopy
- TFA, trifluoroacetic acid
- UV, ultraviolet
- fAβ1–42, HiLyte Fluor488 labelled human Aβ1–42
- β-Sheet
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Affiliation(s)
- Pol Picón-Pagès
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Bonet
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier García-García
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joan Garcia-Buendia
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniela Gutierrez
- Cell Signaling Laboratory, Centro UC de Envejecimiento y Regeneración (CARE), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Valle
- Laboratory of Proteomics and Protein Chemistry, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Carmen E.S. Gómez-Casuso
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Valeriya Sidelkivska
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alejandra Alvarez
- Cell Signaling Laboratory, Centro UC de Envejecimiento y Regeneración (CARE), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Perálvarez-Marín
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Albert Suades
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, ES-08028 Barcelona, Spain
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, ES-08036 Barcelona, Spain
| | - David Andreu
- Laboratory of Proteomics and Protein Chemistry, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Rubén Vicente
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Baldomero Oliva
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco J. Muñoz
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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