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Ayagama T, Charles PD, Bose SJ, Boland B, Priestman DA, Aston D, Berridge G, Fischer R, Cribbs AP, Song Q, Mirams GR, Amponsah K, Heather L, Galione A, Herring N, Kramer H, Capel RA, Platt FM, Schotten U, Verheule S, Burton RA. Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation. iScience 2024; 27:109609. [PMID: 38827406 PMCID: PMC11141153 DOI: 10.1016/j.isci.2024.109609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/07/2024] [Accepted: 03/25/2024] [Indexed: 06/04/2024] Open
Abstract
Endolysosomes (EL) are known for their role in regulating both intracellular trafficking and proteostasis. EL facilitate the elimination of damaged membranes, protein aggregates, membranous organelles and play an important role in calcium signaling. The specific role of EL in cardiac atrial fibrillation (AF) is not well understood. We isolated atrial EL organelles from AF goat biopsies and conducted a comprehensive integrated omics analysis to study the EL-specific proteins and pathways. We also performed electron tomography, protein and enzyme assays on these biopsies. Our results revealed the upregulation of the AMPK pathway and the expression of EL-specific proteins that were not found in whole tissue lysates, including GAA, DYNLRB1, CLTB, SIRT3, CCT2, and muscle-specific HSPB2. We also observed structural anomalies, such as autophagic-vacuole formation, irregularly shaped mitochondria, and glycogen deposition. Our results provide molecular information suggesting EL play a role in AF disease process over extended time frames.
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Affiliation(s)
- Thamali Ayagama
- Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Samuel J. Bose
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Barry Boland
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | | | - Daniel Aston
- Department of Anaesthesia and Critical Care, Royal Papworth Hospital NHS Foundation Trust, Papworth Road, Cambridge CB2 0AY, UK
| | | | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Adam P. Cribbs
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Headington OX3 7LD, UK
| | - Qianqian Song
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Gary R. Mirams
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kwabena Amponsah
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Lisa Heather
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Neil Herring
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Holger Kramer
- Mass spectrometry Facility, The MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | - Ulrich Schotten
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Sander Verheule
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Rebecca A.B. Burton
- Department of Pharmacology, University of Oxford, Oxford, UK
- University of Liverpool, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, Liverpool, UK
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Somerville EN, Krohn L, Senkevich K, Yu E, Ahmad J, Asayesh F, Ruskey JA, Speigelman D, Fahn S, Waters C, Sardi SP, Alcalay RN, Gan-Or Z. Genome-wide association study of glucocerebrosidase activity modifiers. RESEARCH SQUARE 2024:rs.3.rs-4425669. [PMID: 38883744 PMCID: PMC11177962 DOI: 10.21203/rs.3.rs-4425669/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
One of the most common genetic risk factors for Parkinson's disease (PD) are variants in GBA1 , which encodes the lysosomal enzyme glucocerebrosidase (GCase). GCase deficiency has been associated with an increased PD risk, but not all individuals with low GCase activity are carriers of GBA1 mutations, suggesting other factors may be acting as modifiers. We aimed to discover common variants associated with GCase activity, as well as replicate previously reported associations, by performing a genome-wide association study using two independent cohorts: a Columbia University cohort consisting of 697 PD cases and 347 controls and the Parkinson's Progression Markers Initiative (PPMI) cohort consisting of 357 PD cases and 163 controls. As expected, GBA1 variants have the strongest association with decreased activity, led by p.N370S (beta = -4.36, se = 0.32, p = 5.05e-43). We also identify a novel association in the GAA locus (encoding for acid alpha-glucosidase, beta = -0.96, se = 0.17, p = 5.23e-09) that may be the result of an interaction between GCase and acid alpha-glucosidase based on various interaction analyses. Lastly, we show that several PD-risk loci are potentially associated with GCase activity. Further research will be needed to replicate and validate our findings and to uncover the functional connection between acid alpha-glucosidase and GCase.
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Kaya S, Tatar-Yılmaz G, Aktar BSK, Emre EEO. Discovery of New Dual-Target Agents Against PPAR-γ and α-Glucosidase Enzymes with Molecular Modeling Methods: Molecular Docking, Molecular Dynamic Simulations, and MM/PBSA Analysis. Protein J 2024; 43:577-591. [PMID: 38642318 DOI: 10.1007/s10930-024-10196-y] [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] [Accepted: 03/23/2024] [Indexed: 04/22/2024]
Abstract
Type 2 diabetes mellitus (T2DM) has become a serious public health problem both in our country and worldwide, being the most prevalent type of diabetes. The combined use of drugs in the treatment of T2DM leads to serious side effects, including gastrointestinal problems, liver toxicity, hypoglycemia, and treatment costs. Hence, there has been a growing emphasis on drugs that demonstrate dual interactions. Several studies have suggested that dual-target agents for peroxisome proliferator-activated receptor-γ (PPAR-γ) and alpha-glucosidase (α-glucosidase) could be a potent approach for treating patients with diabetes. We aim to develop new antidiabetic agents that target PPAR-γ and α-glucosidase enzymes using molecular modeling techniques. These compounds show dual interactions, are more effective, and have fewer side effects. The molecular docking method was employed to investigate the enzyme-ligand interaction mechanisms of 159 newly designed compounds with target enzymes. Additionally, we evaluated the ADME properties and pharmacokinetic suitability of these compounds based on Lipinski and Veber's rules. Compound 70, which exhibited favorable ADME properties, demonstrated more effective binding energy with both PPAR-γ and α-glucosidase enzymes (-12,16 kcal/mol, -10.07 kcal/mol) compared to the reference compounds of Acetohexamide (-9.31 kcal/mol, -7.48 kcal/mol) and Glibenclamide (-11.12 kcal/mol, -8.66 kcal/mol). Further, analyses of MM/PBSA binding free energy and molecular dynamics (MD) simulations were conducted for target enzymes with compound 70, which exhibited the most favorable binding affinities with both enzymes. Based on this information, our study aims to contribute to the development of new dual-target antidiabetic agents with improved efficacy, reduced side effects, and enhanced reliability for diabetes treatment.
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Affiliation(s)
- Süleyman Kaya
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Gizem Tatar-Yılmaz
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey.
| | - Bedriye Seda Kurşun Aktar
- Department of Hair Care and Beauty Services, Yeşilyurt Vocational School, Malatya Turgut Özal University, 44900, Malatya, Turkey
| | - Emine Elçin Oruç Emre
- Department of Chemistry, Faculty of Art and Sciences, Gaziantep University, Gaziantep, 27310, Turkey
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Elkhawas Y, Gad HA, AbdelRazek MMM, Mandour AA, Bishr MM, Al Musayeib NM, Ashour ML, Khalil N. LC-ESI-MS/MS-Based Comparative Metabolomic Study, Antioxidant and Antidiabetic Activities of Three Lobelia Species: Molecular Modeling and ADMET Study. ACS OMEGA 2024; 9:20477-20487. [PMID: 38737064 PMCID: PMC11079896 DOI: 10.1021/acsomega.4c01587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024]
Abstract
The hydroethanol (70%) extracts of three Lobelia species (L. nicotianifolia, L. sessilifolia, and L. chinensis) were analyzed using LC-ESI-MS/MS. Forty-five metabolites were identified, including different flavonoids, coumarin, polyacetylenes, and alkaloids, which were the most abundant class. By applying Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) based on LC-ESI-MS/MS analysis, the three species were completely segregated from each other. In addition, the three Lobelia extracts were tested for their antioxidant activities using a DPPH assay and as antidiabetic agents against α-glycosidase and α-amylase enzymes. L. chinensis extract demonstrated significant antioxidant activity with an IC50 value of 1.111 mg/mL, while L. nicotianifolia showed mild suppressing activity on the α-glycosidase activity with an IC50 value of 270.8 μg/mL. A molecular simulation study was performed on the main compounds to predict their potential antidiabetic activity and pharmacokinetic properties. The molecular docking results confirmed the α-glycosidase inhibitory activity of the tested compounds, as seen in their binding mode to the key amino acid residues at the binding site compared to that of the standard drug acarbose. Furthermore, the predictive ADMET results revealed good pharmacokinetic properties of almost all of the tested compounds. The biological evaluation results demonstrated the promising activity of the tested compounds, aligned with the in silico results.
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Affiliation(s)
- Yasmin
A. Elkhawas
- Department
of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt
| | - Haidy A. Gad
- Department
of Pharmacognosy, Faculty of Pharmacy, Ain
Shams University, Cairo 11566, Egypt
| | - Mohamed M. M. AbdelRazek
- Department
of Pharmacognosy, Faculty of Pharmacy, Badr
University in Cairo (BUC), Cairo 11829, Egypt
| | - Asmaa A. Mandour
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt
| | - Mokhtar M. Bishr
- Plant
General Manager and Technical Director, Mepaco Co., Enshas AR Raml, Bilbeis, Sharkeiya 11361, Egypt
| | - Nawal M. Al Musayeib
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh 11495, Saudi Arabia
| | - Mohamed L. Ashour
- Department
of Pharmacognosy, Faculty of Pharmacy, Ain
Shams University, Cairo 11566, Egypt
| | - Noha Khalil
- Department
of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Future University in Egypt, Cairo 11835, Egypt
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Zhang N, Liu F, Zhao Y, Sun X, Wen B, Lu JQ, Yan C, Li D. Defect in degradation of glycogenin-exposed residual glycogen in lysosomes is the fundamental pathomechanism of Pompe disease. J Pathol 2024; 263:8-21. [PMID: 38332735 DOI: 10.1002/path.6255] [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: 05/13/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 02/10/2024]
Abstract
Pompe disease is a lysosomal storage disorder that preferentially affects muscles, and it is caused by GAA mutation coding acid alpha-glucosidase in lysosome and glycophagy deficiency. While the initial pathology of Pompe disease is glycogen accumulation in lysosomes, the special role of the lysosomal pathway in glycogen degradation is not fully understood. Hence, we investigated the characteristics of accumulated glycogen and the mechanism underlying glycophagy disturbance in Pompe disease. Skeletal muscle specimens were obtained from the affected sites of patients and mouse models with Pompe disease. Histological analysis, immunoblot analysis, immunofluorescence assay, and lysosome isolation were utilized to analyze the characteristics of accumulated glycogen. Cell culture, lentiviral infection, and the CRISPR/Cas9 approach were utilized to investigate the regulation of glycophagy accumulation. We demonstrated residual glycogen, which was distinguishable from mature glycogen by exposed glycogenin and more α-amylase resistance, accumulated in the skeletal muscle of Pompe disease. Lysosome isolation revealed glycogen-free glycogenin in wild type mouse lysosomes and variously sized glycogenin in Gaa-/- mouse lysosomes. Our study identified that a defect in the degradation of glycogenin-exposed residual glycogen in lysosomes was the fundamental pathological mechanism of Pompe disease. Meanwhile, glycogenin-exposed residual glycogen was absent in other glycogen storage diseases caused by cytoplasmic glycogenolysis deficiencies. In vitro, the generation of residual glycogen resulted from cytoplasmic glycogenolysis. Notably, the inhibition of glycogen phosphorylase led to a reduction in glycogenin-exposed residual glycogen and glycophagy accumulations in cellular models of Pompe disease. Therefore, the lysosomal hydrolysis pathway played a crucial role in the degradation of residual glycogen into glycogenin, which took place in tandem with cytoplasmic glycogenolysis. These findings may offer a novel substrate reduction therapeutic strategy for Pompe disease. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Na Zhang
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital, Shandong University, Jinan, PR China
| | - Fuchen Liu
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital, Shandong University, Jinan, PR China
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital, Shandong University, Jinan, PR China
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Xiaohan Sun
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital, Shandong University, Jinan, PR China
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Bing Wen
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital, Shandong University, Jinan, PR China
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, PR China
| | - Jian-Qiang Lu
- Department of Pathology and Molecular Medicine, Division of Neuropathology, McMaster University, Hamilton, Ontario, Canada
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital, Shandong University, Jinan, PR China
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, PR China
- Qingdao Key Laboratory of Rare Diseases, Qilu Hospital (Qingdao) of Shandong University, Qingdao, PR China
| | - Duoling Li
- Research Institute of Neuromuscular and Neurodegenerative Diseases, Qilu Hospital, Shandong University, Jinan, PR China
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, PR China
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Moussa AY, Alanzi A, Luo J, Chung SK, Xu B. Potential anti-obesity effect of saponin metabolites from adzuki beans: A computational approach. Food Sci Nutr 2024; 12:3612-3627. [PMID: 38726452 PMCID: PMC11077217 DOI: 10.1002/fsn3.4032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 05/12/2024] Open
Abstract
In contrast to its widespread traditional and popular culinary use to reduce weight, Vigna angularis (adzuki beans) was not subjected to sufficient scientific scrutiny. Particularly, its saponins whose role was never investigated before to unveil the beans' antidiabetic and anti-obesity effects. Four vital pancreatic and intestinal carbohydrate enzymes were selected to assess the potency of the triterpenoidal saponins of V. angularis to bind and activate these proteins through high-precision molecular modeling and dynamics mechanisms with accurate molecular mechanics Generalized Born Surface Area (MMGBSA) energy calculations; thus, recognizing their anti-obesity potential. Our results showed that adzukisaponin VI and adzukisaponin IV were the best compounds in the α-amylase and α-glucosidase enzymatic grooves, respectively. Adzukisaponin VI and angulasaponin C were the best fitting in the N-termini of sucrase-isomaltose (SI) enzyme, and angulasaponin C was the best scoring compound in maltase-glucoamylase C-termini. All of them outperformed the standard drug acarbose. These compounds in their protein complexes were selected to undergo molecular simulations of the drug-bound protein compared to the apo-protein through 100 ns, which confirmed the consistency of binding to the key amino acid residues in the four enzyme pockets with the least propensity of unfolding. Detailed analysis is given of the different polar and hydrophobic binding interactions of docked compounds. While maltase-adzukisaponin VI complex scored the lowest MMGBSA free energy of -67.77 Kcal/mol, α-amylase complex with angulasaponin B revealed the free binding energy of -74.18 Kcal/mol with a dominance of van der Waals energy (ΔEVDW) and the least change from the start to the end of the simulation time. This study will direct researchers to the significance of isolating the pure adzuki saponin components to conduct future in vitro and in vivo experimental works and even clinical trials.
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Affiliation(s)
- Ashaimaa Y. Moussa
- Department of Pharmacognosy, Faculty of PharmacyAin Shams UniversityCairoEgypt
| | - Abdullah Alanzi
- Department of Pharmacognosy, College of PharmacyKing Saud UniversityRiyadhSaudi Arabia
| | - Jinhai Luo
- Department of Life Sciences, Food Science and Technology ProgramBNU‐HKBU United International CollegeZhuhaiGuangdongChina
| | - Sookja Kim Chung
- Medical FacultyMacau University of Science and TechnologyMacauChina
| | - Baojun Xu
- Department of Life Sciences, Food Science and Technology ProgramBNU‐HKBU United International CollegeZhuhaiGuangdongChina
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Zheng K, Wu Y, Dai Q, Yan X, Liu Y, Sun D, Yu Z, Jiang S, Ma Q, Jiang W. Extraction, identification, and molecular mechanisms of α-glucosidase inhibitory peptides from defatted Antarctic krill (Euphausia superba) powder hydrolysates. Int J Biol Macromol 2024; 266:131126. [PMID: 38527682 DOI: 10.1016/j.ijbiomac.2024.131126] [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: 09/04/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
The objective of this study was to explore the potential of Antarctic krill-derived peptides as α-glucosidase inhibitors for the treatment of type 2 diabetes. The enzymolysis conditions of α-glucosidase inhibitory peptides were optimized by response surface methodology (RSM), a statistical method that efficiently determines optimal conditions with a limited number of experiments. Gel chromatography and LC-MS/MS techniques were utilized to determine the molecular weight (Mw) distribution and sequences of the hydrolysates. The identification and analysis of the mechanism behind α-glucosidase inhibitory peptides were conducted through conventional and computer-assisted techniques. The binding affinities between peptides and α-glucosidase were further validated using BLI (biolayer interferometry) assay. The results revealed that hydrolysates generated by neutrase exhibited the highest α-glucosidase inhibition rate. Optimal conditions for hydrolysis were determined to be an enzyme concentration of 6 × 103 U/g, hydrolysis time of 5.4 h, and hydrolysis temperature of 45 °C. Four peptides (LPFQR, PSFD, PSFDF, VPFPR) with strong binding affinities to the active site of α-glucosidase, primarily through hydrogen bonding and hydrophobic interactions. This study highlights the prospective utility of Antarctic krill-derived peptides in curtailing α-glucosidase activity, offering a theoretical foundation for the development of novel α-glucosidase inhibitors and related functional foods to enhance diabetes management.
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Affiliation(s)
- Kewei Zheng
- Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yuanyuan Wu
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316022, China
| | - Qingfei Dai
- Marine Science College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaojun Yan
- Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316022, China; Marine Science College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yu Liu
- Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316022, China
| | - Di Sun
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhongjie Yu
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316022, China
| | - Shuoqi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qingbao Ma
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Wei Jiang
- Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan 316022, China.
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Gu X, Kovacs AS, Myung Y, Ascher DB. Mutations in Glycosyltransferases and Glycosidases: Implications for Associated Diseases. Biomolecules 2024; 14:497. [PMID: 38672513 PMCID: PMC11048727 DOI: 10.3390/biom14040497] [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: 12/12/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Glycosylation, a crucial and the most common post-translational modification, coordinates a multitude of biological functions through the attachment of glycans to proteins and lipids. This process, predominantly governed by glycosyltransferases (GTs) and glycoside hydrolases (GHs), decides not only biomolecular functionality but also protein stability and solubility. Mutations in these enzymes have been implicated in a spectrum of diseases, prompting critical research into the structural and functional consequences of such genetic variations. This study compiles an extensive dataset from ClinVar and UniProt, providing a nuanced analysis of 2603 variants within 343 GT and GH genes. We conduct thorough MTR score analyses for the proteins with the most documented variants using MTR3D-AF2 via AlphaFold2 (AlphaFold v2.2.4) predicted protein structure, with the analyses indicating that pathogenic mutations frequently correlate with Beta Bridge secondary structures. Further, the calculation of the solvent accessibility score and variant visualisation show that pathogenic mutations exhibit reduced solvent accessibility, suggesting the mutated residues are likely buried and their localisation is within protein cores. We also find that pathogenic variants are often found proximal to active and binding sites, which may interfere with substrate interactions. We also incorporate computational predictions to assess the impact of these mutations on protein function, utilising tools such as mCSM to predict the destabilisation effect of variants. By identifying these critical regions that are prone to disease-associated mutations, our study opens avenues for designing small molecules or biologics that can modulate enzyme function or compensate for the loss of stability due to these mutations.
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Affiliation(s)
- Xiaotong Gu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4000, Australia; (X.G.); (A.S.K.); (Y.M.)
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Aaron S. Kovacs
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4000, Australia; (X.G.); (A.S.K.); (Y.M.)
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Yoochan Myung
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4000, Australia; (X.G.); (A.S.K.); (Y.M.)
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4000, Australia; (X.G.); (A.S.K.); (Y.M.)
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
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9
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Maulana AF, Maksum IP, Sriwidodo S, Rukayadi Y. Proposed molecular mechanism of non-competitive inhibition using molecular dynamics simulations between α-glucosidase enzyme and mangostin compound as antidiabetic. J Mol Model 2024; 30:136. [PMID: 38634946 DOI: 10.1007/s00894-024-05934-z] [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: 01/09/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
CONTEXT Further understanding of the molecular mechanisms is necessary since it is important for designing new drugs. This study aimed to understand the molecular mechanisms involved in the design of drugs that are inhibitors of the α-glucosidase enzyme. This research aims to gain further understanding of the molecular mechanisms underlying antidiabetic drug design. The molecular docking process yielded 4 compounds with the best affinity energy, including γ-Mangostin, 1,6-dimethyl-ester-3-isomangostin, 1,3,6-trimethyl-ester-α-mangostin, and 3,6,7-trimethyl-ester-γ-mangostin. Free energy calculation with molecular mechanics with generalized born and surface area solvation indicated that the 3,6,7-trimethyl-γ-mangostin had a better free energy value compared to acarbose and simulated maltose together with 3,6,7-trimethyl-γ-mangostin compound. Based on the analysis of electrostatic, van der Waals, and intermolecular hydrogen interactions, 3,6,7-trimethyl-γ-mangostin adopts a noncompetitive inhibition mechanism, whereas acarbose adopts a competitive inhibition mechanism. Consequently, 3,6,7-trimethyl-ester-γ-mangostin, which is a derivative of γ-mangostin, can provide better activity in silico with molecular docking approaches and molecular dynamics simulations. METHOD This research commenced with retrieving protein structures from the RCSB database, generating the formation of ligands using the ChemDraw Professional software, conducting molecular docking with the Autodock Vina software, and performing molecular dynamics simulations using the Amber software, along with the evaluation of RMSD values and intermolecular hydrogen bonds. Free energy, electrostatic interactions, and Van der Waals interaction were calculated using MM/GBSA. Acarbose, used as a positive control, and maltose are simulated together with test compound that has the best free energy. The forcefields used for molecular dynamics simulations are ff19SB, gaff2, and tip3p.
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Affiliation(s)
- Ahmad Fariz Maulana
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jatinangor, Sumedang, 45363, Indonesia
| | - Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jatinangor, Sumedang, 45363, Indonesia.
| | - Sriwidodo Sriwidodo
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Padjadjaran University, Jatinangor, Sumedang, 45363, Indonesia
| | - Yaya Rukayadi
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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10
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Batinić P, Jovanović A, Stojković D, Zengin G, Cvijetić I, Gašić U, Čutović N, Pešić MB, Milinčić DD, Carević T, Marinković A, Bugarski B, Marković T. Phytochemical Analysis, Biological Activities, and Molecular Docking Studies of Root Extracts from Paeonia Species in Serbia. Pharmaceuticals (Basel) 2024; 17:518. [PMID: 38675478 PMCID: PMC11054981 DOI: 10.3390/ph17040518] [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: 02/29/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Without being aware of their chemical composition, many cultures have used herbaceous peony roots for medicinal purposes. Modern phytopreparations intended for use in human therapy require specific knowledge about the chemistry of peony roots and their biological activities. In this study, ethanol-water extracts were prepared by maceration and microwave- and ultrasound-assisted extractions (MAE and UAE, respectively) in order to obtain bioactive molecules from the roots of Paeonia tenuifolia L., Paeonia peregrina Mill., and Paeonia officinalis L. wild growing in Serbia. Chemical characterization; polyphenol and flavonoid content; antioxidant, multianti-enzymatic, and antibacterial activities of extracts; and in vitro gastrointestinal digestion (GID) of hot water extracts were performed. The strongest anti-cholinesterase activity was observed in PT extracts. The highest anti-ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical potential was observed in PP extracts, whereas against DPPH (2,2-diphenyl-1-picrylhydrazyl radicals), the best results were achieved with PO extracts. Regarding antibacterial activity, extracts were strongly potent against Bacillus cereus. A molecular docking simulation was conducted to gather insights into the binding affinity and interactions of polyphenols and other Paeonia-specific molecules in the active sites of tested enzymes. In vitro GID of Paeonia teas showed a different recovery and behavior of the individual bioactives, with an increased recovery of methyl gallate and digallate and a decreased recovery of paeoniflorin and its derivatives. PT (Gulenovci) and PP (Pirot) extracts obtained by UAE and M were more efficient in the majority of the bioactivity assays. This study represents an initial step toward the possible application of Paeonia root extracts in pharmacy, medicine, and food technologies.
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Affiliation(s)
- Petar Batinić
- Institute for Medicinal Plant Research “Dr Josif Pančić”, Tadeuša Košćuška 1, 11000 Belgrade, Serbia; (N.Č.); (T.M.)
| | - Aleksandra Jovanović
- Institute for the Application of Nuclear Energy INEP, University of Belgrade, Banatska 31b, Zemun, 11080 Belgrade, Serbia;
| | - Dejan Stojković
- Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (D.S.); (U.G.); (T.C.)
| | - Gökhan Zengin
- Science Faculty, Selcuk University, 42130 Konya, Turkey;
| | - Ilija Cvijetić
- Faculty of Chemistry, University of Belgrade, Students Square 10-13, 11000 Belgrade, Serbia;
| | - Uroš Gašić
- Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (D.S.); (U.G.); (T.C.)
| | - Natalija Čutović
- Institute for Medicinal Plant Research “Dr Josif Pančić”, Tadeuša Košćuška 1, 11000 Belgrade, Serbia; (N.Č.); (T.M.)
| | - Mirjana B. Pešić
- Faculty of Agriculture, Institute of Food Technology and Biochemistry, University of Belgrade, Nemanjina 6, Zemun, 11080 Belgrade, Serbia; (M.B.P.); (D.D.M.)
| | - Danijel D. Milinčić
- Faculty of Agriculture, Institute of Food Technology and Biochemistry, University of Belgrade, Nemanjina 6, Zemun, 11080 Belgrade, Serbia; (M.B.P.); (D.D.M.)
| | - Tamara Carević
- Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (D.S.); (U.G.); (T.C.)
| | - Aleksandar Marinković
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11000 Belgrade, Serbia; (A.M.); (B.B.)
| | - Branko Bugarski
- Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11000 Belgrade, Serbia; (A.M.); (B.B.)
| | - Tatjana Marković
- Institute for Medicinal Plant Research “Dr Josif Pančić”, Tadeuša Košćuška 1, 11000 Belgrade, Serbia; (N.Č.); (T.M.)
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11
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Üst Ö, Yalçin E, Çavuşoğlu K, Özkan B. LC-MS/MS, GC-MS and molecular docking analysis for phytochemical fingerprint and bioactivity of Beta vulgaris L. Sci Rep 2024; 14:7491. [PMID: 38553576 PMCID: PMC10980731 DOI: 10.1038/s41598-024-58338-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
The plants that we consume in our daily diet and use as a risk preventer against many diseases have many biological and pharmacological activities. In this study, the phytochemical fingerprint and biological activities of Beta vulgaris L. leaf extract, which are widely consumed in the Black Sea region, were investigated. The leaf parts of the plant were dried in an oven at 35 °C and then ground into powder. The main constituents in B. vulgaris were identified by LC-MS/MS and GC-MS analyses. Phenolic content, betaxanthin and betacyanin levels were investigated in the extracts obtained using three different solvents. The biological activity of the extract was investigated by anti-microbial, anti-mutagenic, anti-proliferative and anti-diabetic activity tests. Anti-diabetic activity was investigated by in vitro enzyme inhibition and in-silico molecular docking was performed to confirm this activity. In the LC-MS analysis of B. vulgaris extract, a major proportion of p_coumaric acid, vannilin, protecatechuic aldehyde and sesamol were detected, while the major essential oils determined by GC-MS analysis were hexahydrofarnesyl acetone and phytol. Among the solvents used, the highest extraction efficiency of 2.4% was obtained in methanol extraction, and 36.2 mg of GAE/g phenolic substance, 5.1 mg/L betacyanin and 4.05 mg/L betaxanthin were determined in the methanol extract. Beta vulgaris, which exhibited broad-spectrum anti-microbial activity by forming a zone of inhibition against all tested bacteria, exhibited anti-mutagenic activity in the range of 35.9-61.8% against various chromosomal abnormalities. Beta vulgaris extract, which did not exhibit mutagenic, sub-lethal or lethal effects, exhibited anti-proliferative activity by reducing proliferation in Allium root tip cells by 21.7%. 50 mg/mL B. vulgaris extract caused 58.9% and 55.9% inhibition of α-amylase and α-glucosidase activity, respectively. The interactions of coumaric acid, vanniline, hexahydrofarnesyl acetone and phytol, which are major compounds in phytochemical content, with α-amylase and α-glucosidase were investigated by in silico molecular docking and interactions between molecules via various amino acids were determined. Binding energies between the tested compounds and α-amylase were obtained in the range of - 4.3 kcal/mol and - 6.1 kcal/mol, while for α-glucosidase it was obtained in the range of - 3.7 kcal/mol and - 5.7 kcal/mol. The biological activities of B. vulgaris are closely related to the active compounds it contains, and therefore studies investigating the phytochemical contents of plants are very important. Safe and non-toxic plant extracts can help reduce the risk of various diseases, such as diabetes, and serve as an alternative or complement to current pharmaceutical practices.
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Affiliation(s)
- Özge Üst
- Department of Biology, Institute of Science, Giresun University, Giresun, Turkey
| | - Emine Yalçin
- Department of Biology, Faculty of Science and Art, Giresun University, Giresun, Turkey.
| | - Kültiğin Çavuşoğlu
- Department of Biology, Faculty of Science and Art, Giresun University, Giresun, Turkey
| | - Burak Özkan
- Department of Biology, Institute of Science, Giresun University, Giresun, Turkey
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12
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Zhang M, Niu J, Xu M, Wei E, Liu P, Sheng G. Interplay between mitochondrial dysfunction and lysosomal storage: challenges in genetic metabolic muscle diseases with a focus on infantile onset Pompe disease. Front Cardiovasc Med 2024; 11:1367108. [PMID: 38450370 PMCID: PMC10916335 DOI: 10.3389/fcvm.2024.1367108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
Background Pompe disease (PD) is a rare, progressive autosomal recessive lysosomal storage disorder that directly impacts mitochondrial function, leading to structural abnormalities and potentially culminating in heart failure or cardiogenic shock. The clinical course and molecular mechanisms of the disease remain incompletely understood. Methods We performed a retrospective analysis to examine the clinical manifestations, genetic traits, and the relationship between PD and mitochondrial function in a pediatric patient. This comprehensive evaluation included the use of ultrasound echocardiograms, computed tomography (CT) scans, electrocardiograms, mutagenesis analysis, and structural analysis to gain insights into the patient's condition and the underlying mechanisms of PD. For structural analysis and visualization, the structure of protein data bank ID 5KZX of human GAA was used, and VMD software was used for visualization and analysis. Results The study revealed that a 5-month-old male infant was admitted due to fever, with physical examination finding abnormal cardiopulmonary function and hepatomegaly. Laboratory tests and echocardiography confirmed heart failure and hypertrophic cardiomyopathy. Despite a week of treatment, which normalized body temperature and reduced pulmonary inflammation, cardiac abnormalities did not show significant improvement. Further genetic testing identified a homozygous mutation c.2662G>T (p.E888) in the GAA gene, leading to a diagnosis of Infantile-Onset Pompe Disease (IOPD). Conclusions Although enzyme replacement therapy can significantly improve the quality of life for patients with PD, enhancing mitochondrial function may represent a new therapeutic strategy for treating PD.
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Affiliation(s)
| | | | | | | | | | - Guangyao Sheng
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Ait Lahcen M, Adardour M, Mortada S, Oubahmane M, Hmaimou S, Loughzail M, Hdoufane I, Lahmidi S, Faouzi MEA, Cherqaoui D, Mague JT, Baouid A. Synthesis, characterization, X-ray, α-glucosidase inhibition and molecular docking study of new triazolic systems based on 1,5-benzodiazepine via 1,3-dipolar cycloaddition reactions. J Biomol Struct Dyn 2024; 42:1985-1998. [PMID: 37098807 DOI: 10.1080/07391102.2023.2203263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023]
Abstract
We report in this work a synthesis of novel triazolo[1,5]benzodiazepine derivatives by the 1,3-dipolar cycloaddition reaction of N-aryl-C-ethoxycarbonylnitrilimines with 1,5-benzodiazepines. All the structures of the new compounds were determined from their NMR (1H and 13C) and HRMS. Then, X-ray crystallography analysis of compound 4d confirmed the stereochemistry of cycloadducts. The compounds 1, 4a-d, 5a-d, 6c, 7 and 8 were evaluated for their in vitro anti-diabetic activity against α-glucosidase. The compounds 1, 4d, 5a and 5b showed potential inhibitory activities compared to standard acarbose. Additionally, an in silico docking study was conducted to look into the active binding mode of the synthesized compounds within the target enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Marouane Ait Lahcen
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Mohamed Adardour
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Salma Mortada
- Laboratory of Pharmacology and Toxicology, Biopharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Mehdi Oubahmane
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Samir Hmaimou
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Mohamed Loughzail
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Ismail Hdoufane
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Sanae Lahmidi
- Laboratoire de Chimie Organique Hétérocyclique, Centre de Recherche des Sciences des Médicaments, Pôle de Compétences Pharmacochimie, URAC 21, Faculté des Sciences, Mohammed V University Rabat, Rabat, Morocco
| | - My El Abbes Faouzi
- Laboratory of Pharmacology and Toxicology, Biopharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Driss Cherqaoui
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Abdesselam Baouid
- Molecular Chemistry Laboratory, Department of Chemistry, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
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Kamat V, Barretto DA, Poojary B, Kumar A, Patil VB, Hamzad S. In vitro α-amylase and α-glucosidase inhibition study of dihydropyrimidinones synthesized via one-pot Biginelli reaction in the presence of a green catalyst. Bioorg Chem 2024; 143:107085. [PMID: 38183681 DOI: 10.1016/j.bioorg.2023.107085] [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: 11/02/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
A green catalyst WELPSA-catalyzed three-component condensation (Biginelli) process involving an aldehyde, barbituric/thiobarbituric/1,3-dimethylbarbituric acid, and urea/thiourea/guanidine hydrochloride in a single pot in presence of a green solvent for the production of DHPM have been presented. The catalyst is reusable and this methodology is scalable. By using the in vitro experiments, the antidiabetic potentiality of synthesized compounds that inhibit α-amylase along with α-glucosidase efficiencies was assessed. All the synthesized compounds except for 4a and 4e, showed the most significant inhibition for α-amylase and α-glucosidase activities. Among the synthesized DHPM compounds, 4c and 4b exhibited significant inhibition profiles compared to the standard antidiabetic drug acarbose. Furthermore, synthesized substances' energy-minimized structures, 3D structures, and DFT calculations were performed using Gaussian 09 software, hybrid models, and MM2 force approaches. Strong hydrogen bonds with amino acid residues Arg-672, Arg-600, Trp-613, Asp-404, Asp-282, and Asp-616 indicate that an α-glucosidase-inhibitory peptide may have hypoglycemic efficacy confirmed by the molecular docking study of the synthesized DHPM.
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Affiliation(s)
- Vinuta Kamat
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Kanakapura, Bangalore, Karnataka 562112, India.
| | - Delicia A Barretto
- School of Chemical Sciences, Goa University, Taleigao Plateau-403206, Panaji, Goa, India
| | - Boja Poojary
- Department of Post-Graduate Studies & Research in Chemistry, Mangalore University, Mangalagangothri-574199, Dakshina Kannada, Karnataka, India
| | - Amit Kumar
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Kanakapura, Bangalore, Karnataka 562112, India.
| | - Veerabhadragouda B Patil
- Institute of Energetic Materials, Faculty of Chemical Technology, University of Pardubice, Czech Republic
| | - Shanavaz Hamzad
- Department of Chemistry, Faculty of Engineering and Technology, Jain University, Kanakapura Road, Ramanagara (D) 562112, Karnataka, India
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Chavan RS, Khatib NA, Hariprasad M, Patil VS, Redhwan MAM. Synergistic effects of Momordica charantia, Nigella sativa, and Anethum graveolens on metabolic syndrome targets: In vitro enzyme inhibition and in silico analyses. Heliyon 2024; 10:e24907. [PMID: 38304787 PMCID: PMC10830859 DOI: 10.1016/j.heliyon.2024.e24907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
Momordica charantia, Nigella sativa, and Anethum graveolens are established medicinal plants possessing noted anti-diabetic and anti-obesity properties. However, the molecular mechanisms underscoring their inhibitory effects on pancreatic lipase, α-glucosidase, and HMG-CoA reductase remain unexplored. This study aimed to elucidate the efficacy of various NS, MC, and AG blends in modulating the enzymatic activity of pancreatic lipase, HMG-CoA reductase, and a-glucosidase, utilizing an integrative approach combining in vitro assessments and molecular modeling techniques. A factorial design matrix generated eight distinct concentration combinations of NS, MC, and AG, subsequently subjected to in vitro enzyme inhibition assays. Molecular docking analyses using AutoDock Vina, molecular dynamics simulations, MMPBSA calculations, and principal component analysis, were executed with Gromacs to discern the interaction dynamics between the compounds and target enzymes. A formulation comprising NS:MC:AG at a 215:50:35 μg/mL ratio yielded significant inhibition of pancreatic lipase (IC50: 74.26 ± 4.27 μg/mL). Moreover, a concentration combination of 215:80:35 μg/mL effectively inhibited both α-glucosidase (IC50: 66.09 ± 3.98 μg/mL) and HMGCR (IC50: 129.03 μg/mL). Notably, MC-derived compounds exhibited superior binding affinity towards all three enzymes, compared to their reference molecules, with diosgenin, Momordicoside I, and diosgenin displaying binding affinities of -11.0, -8.8, and -7.9 kcal/mol with active site residues of pancreatic lipase, α-glucosidase, and HMGCR, respectively. Further, 100 ns molecular dynamics simulations revealed the formation and stabilization of non-bonded interactions between the compounds and the enzymes' active site residues. Through a synergistic application of in vitro and molecular modeling methodologies, this study substantiated the potent inhibitory activity of the NS:MC:AG blend (at a ratio of 215:80:35 μg/mL) and specific MC compounds against pancreatic lipase, α-glucosidase, and HMGCR. These findings provide invaluable insights into the molecular underpinnings of these medicinal plants' anti-diabetic and anti-obesity effects and may guide future therapeutic development.
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Affiliation(s)
- Rajashekar S. Chavan
- Department of Pharmacology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research, Belagavi 590010, Karnataka, India
| | - Nayeem A. Khatib
- Department of Pharmacology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research, Belagavi 590010, Karnataka, India
| | - M.G Hariprasad
- Department of Pharmacology, KLE College of Pharmacy, Bengaluru, Karnataka, India
| | - Vishal S. Patil
- Department of Pharmacology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research, Belagavi 590010, Karnataka, India
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Abdullah S, Iqbal A, Ashok AK, Kaouche FC, Aslam M, Hussain S, Rahman J, Hayat MM, Ashraf M. Anti-enzymatic and DNA docking studies of montelukast: A multifaceted molecular scaffold with in vitro investigations, molecular expression analysis and molecular dynamics simulations. Heliyon 2024; 10:e24470. [PMID: 38298631 PMCID: PMC10828691 DOI: 10.1016/j.heliyon.2024.e24470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Montelukast, an approved leukotriene receptor 1 (Cys-LT 1) antagonist with anti-inflammatory properties is used for the treatment of asthma and allergic rhinitis. In the present studies, montelukast was subjected to in vitro inhibitory assays followed by kinetic and in silico investigations. Montelukast demonstrated inhibitory activity against yeast α-glucosidase (IC50 44.31 ± 1.21 μM), jack bean urease (JB urease, IC50 8.72 ± 0.23 μM), human placental alkaline phosphatase (hPAP, IC50 17.53 ± 0.19 μM), bovine intestinal alkaline phosphatase (bIAP, IC50 15.18 ± 0.23 μM) and soybean 15-lipoxygenase (15-LOX, IC50 2.41 ± 0.13 μM). Kinetic studies against α-glucosidase and urease enzymes revealed its competitive mode of inhibition. Molecular expression analysis of montelukast in breast cancer cell line MCF-7 down-regulated AP by a factor of 0.27 (5 μM) compared with the 0.26 value for standard inhibitor levamisole (10 μM). Molecular docking estimated a binding affinity ranging -8.82 to -15.65 kcal/mol for the enzymes. Docking against the DNA dodecamer (ID: 1BNA) observed -9.13 kcal/mol via minor groove binding. MD simulations suggested stable binding between montelukast and the target proteins predicting strong inhibitory potential of the ligand. Montelukast features a chloroquinoline, phenyl ring, a cyclopropane group, a carboxylic group and a sulfur atom all of which collectively enhance its inhibitory potential against the said enzymes. These in vitro and computational investigations demonstrate that it is possible and suggested that the interactions of montelukast with more than one targets presented herein may be linked with the side effects presented by this drug and necessitate additional work. The results altogether suggest montelukast as an important structural scaffold possessing multitargeted features and warrant further investigations in repurposing beyond its traditional pharmacological use.
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Affiliation(s)
- Shawana Abdullah
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Ambar Iqbal
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
- Department of Biochemistry and Molecular Biology, Institute of Biochemistry, Biotechnology & Bioinformatics, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Avinash Karkada Ashok
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, 572103, India
| | - Farah Chafika Kaouche
- Department of Chemistry, Faculty of Sciences of Mater, Ibn Khaldoun University, BP 78 Zaaoura, 14000, Tiaret, Algeria
| | - Misbah Aslam
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Safdar Hussain
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Jameel Rahman
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | | | - Muhammad Ashraf
- Institute of Chemistry, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
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Wójciak KM, Kęska P. Biological Activity of Canned Pork Meat Fortified Black Currant Leaf Extract: In Vitro, In Silico, and Molecular Docking Study. Molecules 2023; 28:8009. [PMID: 38138499 PMCID: PMC10745298 DOI: 10.3390/molecules28248009] [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: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The aim of this study was to assess the antioxidant and inhibiting (ACE-I, DPP IV, and alpha-glucosidase) potential of canned meat featuring reduced sodium nitrate content (50 mg/kg) and fortified with freeze-dried currant leaf extract. Research indicates that employing a lyophilizate dose of 150 mg/kg yields optimal benefits in terms of the antioxidant activity of the meat product. Additionally, three highly promising sequences for canned meat were identified via analysis in the BIOPEP database. These sequences are RPPPPPPPPAD, exhibiting DPP-IV inhibiting activity; ARPPPGPPPLGPPPPGP, demonstrating ACE-I inhibiting activity; and PPGPPPPP, displaying alpha-glucosidase inhibiting activity. Using bioinformatics tools, molecular docking was performed by pairing the selected peptides with protein receptors 2QT9, 1O86, and 5NN8, respectively (PDB ID). The examination of the potential of these selected sequences to manifest specific biological activities toward enzymes was based on the free energy value (∆Gbinding). This knowledge can be harnessed for designing functional foods, thereby contributing to the safeguarding of consumer health.
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Affiliation(s)
| | - Paulina Kęska
- Department of Animal Food Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland;
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Hazra S, Aziz A, Sharma S. Identification and screening of potential inhibitors obtained from Plumeria rubra L. compounds against type 2 diabetes mellitus. J Biomol Struct Dyn 2023; 41:10081-10095. [PMID: 36510695 DOI: 10.1080/07391102.2022.2153924] [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: 06/02/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is the inability of the body's cells to retaliate to insulin, which can periodically culminate into absolute insulin deficiency. Hyperinsulinemia can be alleviated by administering oral medications or insulin. Prevailing medicaments engender repercussions with prolonged use, as they transmute to an inefficacious form. Hence, it will be advantageous to design plant-derived antihyperglycemic drugs with remarkable efficacy and safety quotients to address T2DM and associated comorbidities. Based on prior research, we have identified 7 novel phytocompounds from Plumeria rubra L. and 5 co-crystals that serve as an important residence for T2DM. The compounds are assessed for their inhibitory activity and dynamic stability against five major receptors which are responsible for T2DM. Additionally, in silico ADMET assessment followed by GPU-enabled GROMACS was performed on the selected compounds. The results demonstrated that β-d-Hexaglucoside had the highest binding affinity, hydrophobicity and bond length in contrast to all the targeted receptors. β-d-Hexaglucoside was subjected to dynamic simulation to analyze the root mean square deviation and root mean square fluctuation graph rates using the GROMOS force field in GROMACS software. Furthermore, β-d-Hexaglucoside exhibited inhibitory activity against diabetic receptors with a docking score of -9.5 kcal/mol. The current study proposes β-d-Hexaglucoside as a potential candidate for in-vitro or pre-clinical investigations to ameliorate T2DM management.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subhajit Hazra
- University Institute of Pharmaceutical Sciences, Chandigarh University, Gharuan, India
| | - Abdul Aziz
- Department of Pharmaceutics, Gitanjali College of Pharmacy, Kantagoriya, West Bengal, India
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Ojha MD, Yadav A, P H. Analyzing the potential of selected plant extracts and their structurally diverse secondary metabolites for α-glucosidase inhibitory activity: in vitro and in silico approach. J Biomol Struct Dyn 2023; 41:9523-9538. [PMID: 36345773 DOI: 10.1080/07391102.2022.2142847] [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: 07/18/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Inhibiting α-glucosidase activity is a therapeutic method to regulate post-prandial hyperglycemia in humans. Here, in-vitro and in-silico studies were used to find α-glucosidase inhibitory plant secondary metabolites (PSM). Among 408 solvent extracts from 70 plants tested for α-glucosidase inhibition, 174 had IC50 ≤ 3 mg/ml. α-glucosidase inhibitory PSM is found in several plant species and solvent extracts, indicating their diversity. Further, ensemble molecular docking and structural activity relationship analysis supported this hypothesis where the top 100 PSM with the least binding energy (BE) among the 539 PSM belonged to sesquiterpenoids (34%), catechols (11%), flavonoids (9%) and steroidal lactones (8%). Shortlisted 11 PSM were subjected to molecular dynamic simulation. Withanolide J recorded the least BE of -66.424 ± 22.333 kJ/mol, followed by Withacoagulin I (-64.665 ± 24.030 kJ/mol). When different simulation frames were analyzed, PSM of withanolide groups was stabilized in the narrow entrance of the active pocket forming H-bond with LYS156, TYR158, PHE159, PHE303 PRO312, LEU313, ARG315 and PHE134. Similarly, Hydroxytuberosone and 1, 8-Dihydroxy-3-carboxy-9, 10-anthraquinone (DHCA) formed H-bond with ASP307 located on the loop at the entrance of the active pocket. In the case of Neoliquiritin and Kaempferol-3-o-alpha-L-rhamnoside (KALR), glucose moiety interacted with the GLU277 and ASP215 (catalytic amino acid residues) through H-bonds. In addition, these 11 PSM were found to fulfil the criteria of drug-likeness as per Lipinski's rule of five and pharmacokinetic profile. The present study strengthens the library of α-glucosidase inhibitory plants and PSM, providing valuable information for Type-II Diabetes mellitus management.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Monu Dinesh Ojha
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ajay Yadav
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Hariprasad P
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
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20
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Anding A, Kinton S, Baranowski K, Brezzani A, De Busser H, Dufault MR, Finn P, Keefe K, Tetrault T, Li Y, Qiu W, Raes K, Vitse O, Zhang M, Ziegler R, Sardi SP, Hunter B, George K. Increasing Enzyme Mannose-6-Phosphate Levels but Not Miglustat Coadministration Enhances the Efficacy of Enzyme Replacement Therapy in Pompe Mice. J Pharmacol Exp Ther 2023; 387:188-203. [PMID: 37679046 DOI: 10.1124/jpet.123.001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/17/2023] [Accepted: 06/01/2023] [Indexed: 09/09/2023] Open
Abstract
Pompe disease is a rare glycogen storage disorder caused by a deficiency in the lysosomal enzyme acid α-glucosidase, which leads to muscle weakness, cardiac and respiratory failure, and early mortality. Alglucosidase alfa, a recombinant human acid α-glucosidase, was the first approved treatment of Pompe disease, but its uptake into skeletal muscle via the cation-independent mannose-6-phosphate (M6P) receptor (CIMPR) is limited. Avalglucosidase alfa has received marketing authorization in several countries for infantile-onset and/or late-onset Pompe disease. This recently approved enzyme replacement therapy (ERT) was glycoengineered to maximize CIMPR binding through high-affinity interactions with ∼7 bis-M6P moieties. Recently, small molecules like the glucosylceramide synthase inhibitor miglustat were reported to increase the stability of recombinant human acid α-glucosidase, and it was suggested that an increased serum half-life would result in better glycogen clearance. Here, the effects of miglustat on alglucosidase alfa and avalglucosidase alfa stability, activity, and efficacy in Pompe mice were evaluated. Although miglustat increased the stability of both enzymes in fluorescent protein thermal shift assays and when incubated in neutral pH buffer over time, it reduced their enzymatic activity by ∼50%. Improvement in tissue glycogen clearance and transcriptional dysregulation in Pompe mice correlated with M6P levels but not with miglustat coadministration. These results further substantiate the crucial role of CIMPR binding in lysosomal targeting of ERTs. SIGNIFICANCE STATEMENT: This work describes important new insights into the treatment of Pompe disease using currently approved enzyme replacement therapies (ERTs) coadministered with miglustat. Although miglustat increased the stability of ERTs in vitro, there was no positive impact to glycogen clearance and transcriptional correction in Pompe mice. However, increasing mannose-6-phosphate levels resulted in increased cell uptake in vitro and increased glycogen clearance and transcriptional correction in Pompe mice, further underscoring the crucial role of cation-independent mannose-6-phosphate receptor-mediated lysosomal targeting for ERTs.
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Affiliation(s)
- Allyson Anding
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Sofia Kinton
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Kaitlyn Baranowski
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Alexander Brezzani
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Hilde De Busser
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Michael R Dufault
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Patrick Finn
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Kelly Keefe
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Tanya Tetrault
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Yi Li
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Weiliang Qiu
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Katrien Raes
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Olivier Vitse
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Mindy Zhang
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Robin Ziegler
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - S Pablo Sardi
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Bridge Hunter
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Kelly George
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
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21
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Mancini MC, Noland RC, Collier JJ, Burke SJ, Stadler K, Heden TD. Lysosomal glucose sensing and glycophagy in metabolism. Trends Endocrinol Metab 2023; 34:764-777. [PMID: 37633800 PMCID: PMC10592240 DOI: 10.1016/j.tem.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Lysosomes are cellular organelles that function to catabolize both extra- and intracellular cargo, act as a platform for nutrient sensing, and represent a core signaling node integrating bioenergetic cues to changes in cellular metabolism. Although lysosomal amino acid and lipid sensing in metabolism has been well characterized, lysosomal glucose sensing and the role of lysosomes in glucose metabolism is unrefined. This review will highlight the role of the lysosome in glucose metabolism with a focus on lysosomal glucose and glycogen sensing, glycophagy, and lysosomal glucose transport and how these processes impact autophagy and energy metabolism. Additionally, the role of lysosomal glucose metabolism in genetic and metabolic diseases will be briefly discussed.
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Affiliation(s)
- Melina C Mancini
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Robert C Noland
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - J Jason Collier
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Susan J Burke
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | | | - Timothy D Heden
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA.
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22
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Durmaz L, Kiziltas H, Karagecili H, Alwasel S, Gulcin İ. Potential antioxidant, anticholinergic, antidiabetic and antiglaucoma activities and molecular docking of spiraeoside as a secondary metabolite of onion ( Allium cepa). Saudi Pharm J 2023; 31:101760. [PMID: 37693735 PMCID: PMC10485163 DOI: 10.1016/j.jsps.2023.101760] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023] Open
Abstract
Onion contains many dietary and bioactive components including phenolics and flavonoids. Spiraeoside (quercetin-4-O-β-D-glucoside) is one of the most putative flavonoids in onion. Several antioxidant techniques were used in this investigation to assess the antioxidant capabilities of spiraeoside, including 1,1-diphenyl-2-picrylhydrazyl radical (DPPH·) scavenging, N,N-dimethyl-p-phenylenediamine radical (DMPD•+) scavenging, 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulphonate) radical (ABTS•+) scavenging activities, cupric ions (Cu2+) reducing and potassium ferric cyanide reduction abilities. In contrast, the water-soluble α-tocopherol analogue trolox and the conventional antioxidants butylated hydroxytoluene (BHT), butylated hydroxyanisole (BHA), and α-tocopherol were utilized as the standards for evaluation. Spiraeoside scavenged the DPPH radicals an IC50 of 28.51 μg/mL (r2: 0.9705) meanwhile BHA, BHT, trolox, and α-tocopherol displayed IC50 of 10.10 μg/mL (r2: 0.9015), 25.95 μg/mL (r2: 0.9221), 7.059 μg/mL (r2: 0.9614) and 11.31 μg/mL (r2: 0.9642), accordingly. The results exhibited that spiraeoside had effects similar to BHT, but less potent than α-tocopherol, trolox and BHA. Also, inhibitory effects of spiraeoside were evaluated toward some metabolic enzymes including acetylcholinesterase (AChE), butyrylcholinesterase (BChE), carbonic anhydrase II (CA II) and α-glycosidase, which are related to a number of illnesses, such as Alzheimer's disease (AD), diabetes mellitus and glaucoma disorder. Spiraeoside exhibited IC50 values of 4.44 nM (r2: 0.9610), 7.88 nM (r2: 0.9784), 19.42 nM (r2: 0.9673) and 29.17 mM (r2: 0.9209), respectively against these enzymes. Enzyme inhibition abilities were compared to clinical used inhibitors including acetazolamide (for CA II), tacrine (for AChE and BChE) and acarbose (for α-glycosidase). Spiraeoside demonstrated effective antioxidant, anticholinergic, antidiabetic and antiglaucoma activities. With these properties, it has shown that Spiraeoside has the potential to be a medicine for some metabolic diseases.
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Affiliation(s)
- Lokman Durmaz
- Department of Medical Services and Technology, Cayirli Vocational School, Erzincan Binali Yildirim University, 24500, Cayirli, Erzincan, Turkey
| | - Hatice Kiziltas
- Department of Pharmacy Services, Vocational School of Health Services, Van Yuzuncu Yil University, 65080, Van, Turkey
| | - Hasan Karagecili
- Department of Nursing, Faculty of Health Sciences, Siirt University, 56100, Siirt, Turkey
| | - Saleh Alwasel
- King Saud University, College of Science, Department of Zoology, 11362, Riyadh, Saudi Arabia
| | - İlhami Gulcin
- Department of Chemistry, Faculty of Science, Atatürk University, 25240, Erzurum, Turkey
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23
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El-Sayed NNE, Al-Otaibi TM, Barakat A, Almarhoon ZM, Hassan MZ, Al-Zaben MI, Krayem N, Masand VH, Ben Bacha A. Synthesis and Biological Evaluation of Some New 3-Aryl-2-thioxo-2,3-dihydroquinazolin-4(1 H)-ones and 3-Aryl-2-(benzylthio)quinazolin-4(3 H)-ones as Antioxidants; COX-2, LDHA, α-Glucosidase and α-Amylase Inhibitors; and Anti-Colon Carcinoma and Apoptosis-Inducing Agents. Pharmaceuticals (Basel) 2023; 16:1392. [PMID: 37895863 PMCID: PMC10610505 DOI: 10.3390/ph16101392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Oxidative stress, COX-2, LDHA and hyperglycemia are interlinked contributing pathways in the etiology, progression and metastasis of colon cancer. Additionally, dysregulated apoptosis in cells with genetic alternations leads to their progression in malignant transformation. Therefore, quinazolinones 3a-3h and 5a-5h were synthesized and evaluated as antioxidants, enzymes inhibitors and cytotoxic agents against LoVo and HCT-116 cells. Moreover, the most active cytotoxic derivatives were evaluated as apoptosis inducers. The results indicated that 3a, 3g and 5a were efficiently scavenged DPPH radicals with lowered IC50 values (mM) ranging from 0.165 ± 0.0057 to 0.191 ± 0.0099, as compared to 0.245 ± 0.0257 by BHT. Derivatives 3h, 5a and 5h were recognized as more potent dual inhibitors than quercetin against α-amylase and α-glucosidase, in addition to 3a, 3c, 3f and 5b-5f against α-amylase. Although none of the compounds demonstrated a higher efficiency than the reference inhibitors against COX-2 and LDHA, 3a and 3g were identified as the most active derivatives. Molecular docking studies were used to elucidate the binding affinities and binding interactions between the inhibitors and their target proteins. Compounds 3a and 3f showed cytotoxic activities, with IC50 values (µM) of 294.32 ± 8.41 and 383.5 ± 8.99 (LoVo), as well as 298.05 ± 13.26 and 323.59 ± 3.00 (HCT-116). The cytotoxicity mechanism of 3a and 3f could be attributed to the modulation of apoptosis regulators (Bax and Bcl-2), the activation of intrinsic and extrinsic apoptosis pathways via the upregulation of initiator caspases-8 and -9 as well as executioner caspase-3, and the arrest of LoVo and HCT-116 cell cycles in the G2/M and G1 phases, respectively. Lastly, the physicochemical, medicinal chemistry and ADMET properties of all compounds were predicted.
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Affiliation(s)
| | - Taghreed M. Al-Otaibi
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Assem Barakat
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Zainab M. Almarhoon
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Mohd. Zaheen Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia;
| | - Maha I. Al-Zaben
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Najeh Krayem
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS, Université de Sfax, Route de Soukra 3038, Sfax BP 1173, Tunisia;
| | - Vijay H. Masand
- Department of Chemistry, Vidya Bharati College, Camp, Amravati, Maharashtra 444602, India;
| | - Abir Ben Bacha
- Biochemistry Department, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia;
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24
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Désiré J, Debbah Z, Gueyrard D, Marrot J, Blériot Y, Kato A. Evaluation of nonnatural L-iminosugar C,C-glycosides, a new class of C-branched iminosugars, as glycosidase inhibitors. Carbohydr Res 2023; 532:108903. [PMID: 37523839 DOI: 10.1016/j.carres.2023.108903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
Capitalizing on a previously developed Staudinger/azaWittig/Grignard (SAWG)-ring contraction sequence that furnished protected six-membered L-iminosugar C,C-glycosides bearing an allyl group and various substituents at the pseudoanomeric position, the synthesis and glycosidase inhibition of a small library of six- and seven-membered L-iminosugar C,C-glycosides is reported. Their hydrogenolysis or cyclization by RCM followed by deprotection afforded eleven L-iminosugars including spirocyclic derivatives. All compounds adopt a 1C4 conformation in solution according to NMR data. Compared to previously reported branched L-iminosugars, the L-iminosugar C,C-glycosides reported herein were less potent glycosidase inhibitors. However, some of these compounds showed micromolar inhibition of human lysosome β-glucocerebrosidase suggesting that such iminosugars could be useful to access potent CGase inhibitors by adjusting the structure/length of the pseudoanomeric substituents.
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Affiliation(s)
- Jérôme Désiré
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Université de Poitiers, CNRS, Equipe "Synthèse Organique", Groupe Glycochimie, F-86073, Poitiers, France.
| | - Zakaria Debbah
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Université de Poitiers, CNRS, Equipe "Synthèse Organique", Groupe Glycochimie, F-86073, Poitiers, France
| | - David Gueyrard
- Laboratoire Chimie Organique II-Glycochimie - ICBMS - UMR 5246, Université de Lyon - Université Claude Bernard - Lyon 1 Bâtiment Lederer - 1, rue V. Grignard, 69622, Villeurbanne Cedex, France
| | - Jérôme Marrot
- Institut Lavoisier de Versailles, UMR-CNRS 8180, Université de Versailles, 78035, Versailles Cedex, France
| | - Yves Blériot
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Université de Poitiers, CNRS, Equipe "Synthèse Organique", Groupe Glycochimie, F-86073, Poitiers, France
| | - Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
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Musfiroh I, Ifaya M, Sahidin I, Herawati DMD, Tjitraresmi A, Abdurrahman S, Muchtaridi M, Khairul Ikram NK. Isolation of phenolic compound from Lawsonia inermis and its prediction as anti-diabetic agent using molecular docking and molecular dynamic simulation. J Biomol Struct Dyn 2023:1-10. [PMID: 37776010 DOI: 10.1080/07391102.2023.2262595] [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: 06/19/2023] [Accepted: 09/16/2023] [Indexed: 10/01/2023]
Abstract
High blood sugar is a defining feature of chronic disease, diabetes mellitus (DM). There are numerous commercially available medications for the treatment of DM. However, managing the patient's glucose levels remain a challenge because of the gradual reduction in beta-cell function and some side effects from the long-term use of various medications. Previous research has shown that the phenolic compound of henna plant (Lawsonia inermis L.) has the potential as anti-diabetic agent since it is able to suppress the digesting of α-amylase enzyme. In these studies, the plant' phenolic compounds have been isolated and characterized using UV, IR, NMR and LC-MS methods. Furthermore, the compound interaction into the active site of the α-amylase enzyme has been analyzed using molecular docking and molecular dynamics, as well as into α-glucosidase enzyme for predicting of the affinities. The results showed that isolated compound has the molecular formula of C15H10O6 with eleven degrees of unsaturation (DBE; double bond equivalence). The DBE value corresponds to the structure of the luteolin compound having an aromatic ring (8), a carbonyl group on the side chain (1) and a ketone ring with (2). The interaction study of the isolated compound with α-amylase and α-glucosidase enzyme using molecular docking compared to the positive control (acarbose) gave binding energy of -8.03 and -8.95 kcal/mol, respectively. The molecular dynamics simulation using the MM-PBSA method, complex stability based on solvent accessible surface area (SASA), root mean square deviation (RMSD), and root mean square fluctuation (RMSF) revealed that the compound has a high affinity for receptors. The characteristics of skin permeability, absorption, and distribution using ADME-Tox model were also well predicted. The results indicate that the phenolic compound isolated from L. inermis leaf was luteolin and it has the potential as an anti-diabetic agent.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ida Musfiroh
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, Indonesia
| | - Mus Ifaya
- Department of Pharmacy, Faculty of Science and Technology, Universitas Mandala Waluya, Southeast Sulawesi, Indonesia
| | - I Sahidin
- Faculty of Pharmacy, Universitas Halu Oleo Kendari, Southeast Sulawesi, Indonesia
| | - Dewi M D Herawati
- Division of Medical Nutrition, Department of Public Health, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ami Tjitraresmi
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, Indonesia
| | - Syawal Abdurrahman
- Department of Medical Laboratory Technology, Faculty of Science and Technology, Universitas Mandala Waluya, Kendari, Indonesia
| | - Muchtaridi Muchtaridi
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, Indonesia
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26
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Goldstein JL, McGlaughon J, Kanavy D, Goomber S, Pan Y, Deml B, Donti T, Kearns L, Seifert BA, Schachter M, Son RG, Thaxton C, Udani R, Bali D, Baudet H, Caggana M, Hung C, Kyriakopoulou L, Rosenblum L, Steiner R, Pinto E Vairo F, Wang Y, Watson M, Fernandez R, Weaver M, Clarke L, Rehder C. Variant Classification for Pompe disease; ACMG/AMP specifications from the ClinGen Lysosomal Diseases Variant Curation Expert Panel. Mol Genet Metab 2023; 140:107715. [PMID: 37907381 PMCID: PMC10872922 DOI: 10.1016/j.ymgme.2023.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023]
Abstract
Accurate determination of the clinical significance of genetic variants is critical to the integration of genomics in medicine. To facilitate this process, the NIH-funded Clinical Genome Resource (ClinGen) has assembled Variant Curation Expert Panels (VCEPs), groups of experts and biocurators which provide gene- and disease- specifications to the American College of Medical Genetics & Genomics and Association for Molecular Pathology's (ACMG/AMP) variation classification guidelines. With the goal of classifying the clinical significance of GAA variants in Pompe disease (Glycogen storage disease, type II), the ClinGen Lysosomal Diseases (LD) VCEP has specified the ACMG/AMP criteria for GAA. Variant classification can play an important role in confirming the diagnosis of Pompe disease as well as in the identification of carriers. Furthermore, since the inclusion of Pompe disease on the Recommended Uniform Screening Panel (RUSP) for newborns in the USA in 2015, the addition of molecular genetic testing has become an important component in the interpretation of newborn screening results, particularly for asymptomatic individuals. To date, the LD VCEP has submitted classifications and supporting data on 243 GAA variants to public databases, specifically ClinVar and the ClinGen Evidence Repository. Here, we describe the ACMG/AMP criteria specification process for GAA, an update of the GAA-specific variant classification guidelines, and comparison of the ClinGen LD VCEP's GAA variant classifications with variant classifications submitted to ClinVar. The LD VCEP has added to the publicly available knowledge on the pathogenicity of variants in GAA by increasing the number of expert-curated GAA variants present in ClinVar, and aids in resolving conflicting classifications and variants of uncertain clinical significance.
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Affiliation(s)
- Jennifer L Goldstein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | | | - Dona Kanavy
- Duke University Health System, Durham, NC, USA
| | | | | | - Brett Deml
- Prevention Genetics, Marshfield, WI, USA
| | | | - Liz Kearns
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Bryce A Seifert
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | | | - Rachel G Son
- Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rupa Udani
- Wisconsin State Lab of Hygiene at University of Wisconsin, Madison, WI, USA
| | | | - Heather Baudet
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michele Caggana
- Newborn Screening Program, Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | | | | | | | - Robert Steiner
- Prevention Genetics, Marshfield, WI, USA; Medical College of Wisconsin, Brookfield, WI, USA
| | | | | | - Michael Watson
- American College of Medical Genetics and Genomics, Bethesda, MD, USA
| | - Raquel Fernandez
- American College of Medical Genetics and Genomics, Bethesda, MD, USA
| | - Meredith Weaver
- American College of Medical Genetics and Genomics, Bethesda, MD, USA
| | - Lorne Clarke
- University of British Columbia, Vancouver, BC, Canada
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27
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van der Gracht D, Rowland RJ, Roig-Zamboni V, Ferraz MJ, Louwerse M, Geurink PP, Aerts JMFG, Sulzenbacher G, Davies GJ, Overkleeft HS, Artola M. Fluorescence polarisation activity-based protein profiling for the identification of deoxynojirimycin-type inhibitors selective for lysosomal retaining alpha- and beta-glucosidases. Chem Sci 2023; 14:9136-9144. [PMID: 37655021 PMCID: PMC10466331 DOI: 10.1039/d3sc01021j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023] Open
Abstract
Lysosomal exoglycosidases are responsible for processing endocytosed glycans from the non-reducing end to produce the corresponding monosaccharides. Genetic mutations in a particular lysosomal glycosidase may result in accumulation of its particular substrate, which may cause diverse lysosomal storage disorders. The identification of effective therapeutic modalities to treat these diseases is a major yet poorly realised objective in biomedicine. One common strategy comprises the identification of effective and selective competitive inhibitors that may serve to stabilize the proper folding of the mutated enzyme, either during maturation and trafficking to, or residence in, endo-lysosomal compartments. The discovery of such inhibitors is greatly aided by effective screening assays, the development of which is the focus of the here-presented work. We developed and applied fluorescent activity-based probes reporting on either human GH30 lysosomal glucosylceramidase (GBA1, a retaining β-glucosidase) or GH31 lysosomal retaining α-glucosidase (GAA). FluoPol-ABPP screening of our in-house 358-member iminosugar library yielded compound classes selective for either of these enzymes. In particular, we identified a class of N-alkyldeoxynojirimycins that inhibit GAA, but not GBA1, and that may form the starting point for the development of pharmacological chaperone therapeutics for the lysosomal glycogen storage disease that results from genetic deficiency in GAA: Pompe disease.
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Affiliation(s)
- Daniël van der Gracht
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Rhianna J Rowland
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Véronique Roig-Zamboni
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University Marseille France
| | - Maria J Ferraz
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Max Louwerse
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Centre 2333 ZC Leiden The Netherlands
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Gerlind Sulzenbacher
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University Marseille France
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York York YO10 5DD UK
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands
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Labella B, Cotti Piccinelli S, Risi B, Caria F, Damioli S, Bertella E, Poli L, Padovani A, Filosto M. A Comprehensive Update on Late-Onset Pompe Disease. Biomolecules 2023; 13:1279. [PMID: 37759679 PMCID: PMC10526932 DOI: 10.3390/biom13091279] [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: 06/17/2023] [Revised: 08/10/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Pompe disease (PD) is an autosomal recessive disorder caused by mutations in the GAA gene that lead to a deficiency in the acid alpha-glucosidase enzyme. Two clinical presentations are usually considered, named infantile-onset Pompe disease (IOPD) and late-onset Pompe disease (LOPD), which differ in age of onset, organ involvement, and severity of disease. Assessment of acid alpha-glucosidase activity on a dried blood spot is the first-line screening test, which needs to be confirmed by genetic analysis in case of suspected deficiency. LOPD is a multi-system disease, thus requiring a multidisciplinary approach for efficacious management. Enzyme replacement therapy (ERT), which was introduced over 15 years ago, changes the natural progression of the disease. However, it has limitations, including a reduction in efficacy over time and heterogeneous therapeutic responses among patients. Novel therapeutic approaches, such as gene therapy, are currently under study. We provide a comprehensive review of diagnostic advances in LOPD and a critical discussion about the advantages and limitations of current and future treatments.
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Affiliation(s)
- Beatrice Labella
- Department of Clinical and Experimental Sciences, University of Brescia, 25100 Brescia, Italy; (B.L.); (S.C.P.); (A.P.)
- Unit of Neurology, ASST Spedali Civili, 25100 Brescia, Italy;
| | - Stefano Cotti Piccinelli
- Department of Clinical and Experimental Sciences, University of Brescia, 25100 Brescia, Italy; (B.L.); (S.C.P.); (A.P.)
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, 25064 Brescia, Italy; (B.R.); (F.C.); (S.D.); (E.B.)
| | - Barbara Risi
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, 25064 Brescia, Italy; (B.R.); (F.C.); (S.D.); (E.B.)
| | - Filomena Caria
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, 25064 Brescia, Italy; (B.R.); (F.C.); (S.D.); (E.B.)
| | - Simona Damioli
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, 25064 Brescia, Italy; (B.R.); (F.C.); (S.D.); (E.B.)
| | - Enrica Bertella
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, 25064 Brescia, Italy; (B.R.); (F.C.); (S.D.); (E.B.)
| | - Loris Poli
- Unit of Neurology, ASST Spedali Civili, 25100 Brescia, Italy;
| | - Alessandro Padovani
- Department of Clinical and Experimental Sciences, University of Brescia, 25100 Brescia, Italy; (B.L.); (S.C.P.); (A.P.)
- Unit of Neurology, ASST Spedali Civili, 25100 Brescia, Italy;
| | - Massimiliano Filosto
- Department of Clinical and Experimental Sciences, University of Brescia, 25100 Brescia, Italy; (B.L.); (S.C.P.); (A.P.)
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, 25064 Brescia, Italy; (B.R.); (F.C.); (S.D.); (E.B.)
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29
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Wang C, Li YP, Gong X, Gan LS, Zhang H. Rare diphenylheptanoid-phenylheptanoid hybrids with α-glucosidase inhibitory effects from the pollen of Typha angustifolia. Nat Prod Res 2023:1-11. [PMID: 37599620 DOI: 10.1080/14786419.2023.2248352] [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: 05/18/2023] [Revised: 07/20/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023]
Abstract
Two rarely occurring diphenylheptanoid-phenylheptanoid hybrid dimers (1 and 2) and one new oxygenated fatty acid (3), as well as two known fatty acid analogues (4 and 5), were isolated from the 70% EtOH extract of the pollen of Typha angustifolia. Their planar structures were established by interpretation of MS and NMR spectroscopic data, and the absolute configurations of 1 and 2 were determined by Mosher's method and quantum chemical TD-DFT calculations of ECD spectra. An in vitro anti-diabetic evaluation of these isolates revealed that compounds 1 and 2 exhibited promising inhibitory activity against α-glucosidase with IC50 values of 11.85 ± 0.69 and 17.06 ± 3.08 μM, respectively. It is the first report on both diphenylheptanoid constituents and α-glucosidase inhibitors from the title plant, which represents a significant phytochemical progress of this herbal species and may serve as a reference for its future medicinal applications.
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Affiliation(s)
- Chao Wang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yu-Peng Li
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xu Gong
- School of Biotechnology and Health Sciences, International Healthcare Innovation Institute, Wuyi University, Jiangmen, China
| | - Li-She Gan
- School of Biotechnology and Health Sciences, International Healthcare Innovation Institute, Wuyi University, Jiangmen, China
| | - Hua Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, China
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30
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Elhady SS, Alshobaki NM, Elfaky MA, Koshak AE, Alharbi M, Abdelhameed RFA, Darwish KM. Deciphering Molecular Aspects of Potential α-Glucosidase Inhibitors within Aspergillus terreus: A Computational Odyssey of Molecular Docking-Coupled Dynamics Simulations and Pharmacokinetic Profiling. Metabolites 2023; 13:942. [PMID: 37623885 PMCID: PMC10456934 DOI: 10.3390/metabo13080942] [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: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Hyperglycemia, as a hallmark of the metabolic malady diabetes mellitus, has been an overwhelming healthcare burden owing to its high rates of comorbidity and mortality, as well as prospective complications affecting different body organs. Available therapeutic agents, with α-glucosidase inhibitors as one of their cornerstone arsenal, control stages of broad glycemia while showing definitive characteristics related to their low clinical efficiency and off-target complications. This has propelled the academia and industrial section into discovering novel and safer candidates. Herein, we provided a thorough computational exploration of identifying candidates from the marine-derived Aspergillus terreus isolates. Combined structural- and ligand-based approaches using a chemical library of 275 metabolites were adopted for pinpointing promising α-glucosidase inhibitors, as well as providing guiding insights for further lead optimization and development. Structure-based virtual screening through escalating precision molecular docking protocol at the α-glucosidase canonical pocket identified 11 promising top-docked hits, with several being superior to the market drug reference, acarbose. Comprehensive ligand-based investigations of these hits' pharmacokinetics ADME profiles, physiochemical characterizations, and obedience to the gold standard Lipinski's rule of five, as well as toxicity and mutagenicity profiling, proceeded. Under explicit conditions, a molecular dynamics simulation identified the top-stable metabolites: butyrolactone VI (SK-44), aspulvinone E (SK-55), butyrolactone I 4''''-sulfate (SK-72), and terrelumamide B (SK-173). They depicted the highest free binding energies and steadiest thermodynamic behavior. Moreover, great structural insights have been revealed, including the advent of an aromatic scaffold-based interaction for ligand-target complex stability. The significance of introducing balanced hydrophobic/polar moieties, like triazole and other bioisosteres of carboxylic acid, has been highlighted across docking, ADME/Tox profiling, and molecular dynamics studies for maximizing binding interactions while assuring safety and optimal pharmacokinetics for targeting the intestinal-localized α-glucosidase enzyme. Overall, this study provided valuable starting points for developing new α-glucosidase inhibitors based on nature-derived unique scaffolds, as well as guidance for prospective lead optimization and development within future pre-clinical and clinical investigations.
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Affiliation(s)
- Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
| | - Noha M. Alshobaki
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
| | - Mahmoud A. Elfaky
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdulrahman E. Koshak
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (N.M.A.); (M.A.E.); (A.E.K.)
| | - Majed Alharbi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Reda F. A. Abdelhameed
- Department of Pharmacognosy, Faculty of Pharmacy, Galala University, New Galala 43713, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
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31
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Kęska P, Stadnik J, Łupawka A, Michalska A. Novel α-Glucosidase Inhibitory Peptides Identified In Silico from Dry-Cured Pork Loins with Probiotics through Peptidomic and Molecular Docking Analysis. Nutrients 2023; 15:3539. [PMID: 37630730 PMCID: PMC10460020 DOI: 10.3390/nu15163539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Diabetes mellitus is a serious metabolic disorder characterized by abnormal blood glucose levels in the body. The development of therapeutic strategies for restoring and maintaining blood glucose homeostasis is still in progress. Synthetic alpha-amylase and alpha-glucosidase inhibitors can improve blood glucose control in diabetic patients by effectively reducing the risk of postprandial hyperglycemia. Peptides of natural origin are promising compounds that can serve as alpha-glucosidase inhibitors in the treatment of type 2 diabetes. Potential alpha-glucosidase-inhibiting peptides obtained from aqueous and saline extracts from dry-cured pork loins inoculated with probiotic LAB were evaluated using in vitro and in silico methods. To identify the peptide sequences, liquid chromatography-mass spectrometry was used. For this purpose, in silico calculation methods were used, and the occurrence of bioactive fragments in the protein followed the ADMET approach. The most promising sequences were molecularly docked to test their interaction with the human alpha-glycosidase molecule (PDB ID: 5NN8). The docking studies proved that oligopeptides VATPPPPPPPK, DIPPPPM, TPPPPPPG, and TPPPPPPPK obtained by hydrolysis of proteins from ripening dry-cured pork loins showed the potential to bind to the human alpha-glucosidase molecule and may act effectively as a potential antidiabetic agent.
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Affiliation(s)
| | - Joanna Stadnik
- Department of Animal Food Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland
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32
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Nyathi B, Bvunzawabaya JT, Venissa P Mudawarima C, Manzombe E, Tsotsoro K, Selemani MA, Munyuki G, Rwere F. Inhibitory and in silico molecular docking of Xeroderris stuhlmannii (Taub.) Mendonca & E.P. Sousa phytochemical compounds on human α-glucosidases. JOURNAL OF ETHNOPHARMACOLOGY 2023; 312:116501. [PMID: 37100261 DOI: 10.1016/j.jep.2023.116501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 05/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Herbal traditional medicine is used by millions of people in Africa for treatment of ailments such as diabetes mellitus, stomach disorders and respiratory diseases. Xeroderris stuhlmannii (Taub.) Mendonca & E.P. Sousa (X. stuhlmannii (Taub.)) is a medicinal plant used traditionally in Zimbabwe to treat type 2 diabetes mellitus (T2DM) and its complications. However, there is no scientific evidence to support its inhibitory effect against digestive enzymes (α-glucosidases) that are linked to high blood sugar in humans. AIM OF THE STUDY This work aims to investigate whether bioactive phytochemicals of crude X. stuhlmannii (Taub.) can scavenge free radicals and inhibit α-glucosidases in order to reduce blood sugar in humans. MATERIALS AND METHODS Here we examined the free radical scavenging potential of crude aqueous, ethyl acetate and methanolic extracts of X. stuhlmannii (Taub.) using the diphenyl-2-picrylhydrazyl assay in vitro. Furthermore, we carried out in vitro inhibition of α-glucosidases (α-amylase and α-glucosidase) by the crude extracts using chromogenic 3,5-dinitrosalicylic acid and p-nitrophenyl-α-D-glucopyranoside substrates. We also used molecular docking approaches (Autodock Vina) to screen for bioactive phytochemical compounds targeting the digestive enzymes. RESULTS Our results showed that phytochemicals in X. stuhlmannii (Taub.) aqueous, ethyl acetate and methanolic extracts scavenged free radicals with IC50 values ranging from 0.002 to 0.013 μg/mL. Furthermore, crude aqueous, ethyl acetate and methanolic extracts significantly inhibited α-amylase and α-glucosidase with IC50 values of 10.5-29.5 μg/mL (versus 54.1 ± 0.7 μg/mL for acarbose) and 8.8-49.5 μg/mL (versus 161.4 ± 1.8 μg/mL for acarbose), respectively. In silico molecular docking findings and pharmacokinetic predictions showed that myricetin is likely a novel plant-derived α-glucosidase inhibitor. CONCLUSION Collectively, our findings suggest pharmacological targeting of digestive enzymes by X. stuhlmannii (Taub.) crude extracts may reduce blood sugar in humans with T2DM via inhibition of α-glucosidases.
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Affiliation(s)
- Brilliant Nyathi
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Jonathan Tatenda Bvunzawabaya
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe; Department of Chemical Sciences, Faculty of Science and Technology Midlands State University, Private Bag 9055 Senga Road, Gweru, 263, Zimbabwe
| | - Chido Venissa P Mudawarima
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Emily Manzombe
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Kudakwashe Tsotsoro
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Major Allen Selemani
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Gadzikano Munyuki
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Freeborn Rwere
- Department of Chemistry, School of Natural Sciences and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe; Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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33
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Chan MY, Jalil JA, Yakob Y, Wahab SAA, Ali EZ, Khalid MKNM, Leong HY, Chew HB, Sivabalakrishnan JB, Ngu LH. Genotype, phenotype and treatment outcomes of 17 Malaysian patients with infantile-onset Pompe disease and the identification of 3 novel GAA variants. Orphanet J Rare Dis 2023; 18:231. [PMID: 37542277 PMCID: PMC10403872 DOI: 10.1186/s13023-023-02848-6] [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: 06/03/2022] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND Pompe disease is a rare glycogen storage disorder caused by deficiency of the lysosomal enzyme acid alpha-glucosidase (GAA), leading to glycogen deposition in multiple tissues. Infantile-onset Pompe disease (IOPD) patients present within the first year of life with profound hypotonia and hypertrophic cardiomyopathy. Treatment with enzyme replacement therapy (ERT) has significantly improved survival for this otherwise lethal disorder. This study aims to describe the clinical and molecular spectrum of Malaysian IOPD patients, and to analyze their long term treatment outcomes. METHODS Seventeen patients diagnosed with IOPD between 2000 and 2020 were included in this retrospective cohort study. Clinical and biochemical data were collated and analyzed using descriptive statistics. GAA enzyme levels were performed on dried blood spots. Molecular analysis of the GAA gene was performed by polymerase chain reaction and Sanger sequencing. Structural modelling was used to predict the effect of the novel mutations on enzyme structure. RESULTS Our cohort had a median age of presentation of 3 months and median age of diagnosis of 6 months. Presenting features were hypertrophic cardiomyopathy (100%), respiratory insufficiency (94%), hypotonia (88%), failure to thrive (82%), feeding difficulties (76%), and hepatomegaly (76%). Fourteen different mutations in the GAA gene were identified, with three novel mutations, c.1552-14_1552-1del, exons 2-3 deletion and exons 6-10 deletion. The most common mutation identified was c.1935C > A p.(D645E), with an allele frequency of 33%. Sixteen patients received ERT at the median age of 7 months. Overall survival was 29%. Mean age of death was 17.5 months. Our longest surviving patient has atypical IOPD and is currently 20 years old. CONCLUSIONS This is the first study to analyze the genotype and phenotype of Malaysian IOPD patients, and has identified the c.1935C > A p.(D645E) as the most common mutation. The three novel mutations reported in this study expands the mutation spectrum for IOPD. Our low survival rate underscores the importance of early diagnosis and treatment in achieving better treatment outcomes.
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Affiliation(s)
- Mei-Yan Chan
- Department of Genetics, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586, Kuala Lumpur, Malaysia.
| | - Julaina Abdul Jalil
- Unit of Biochemistry, Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Yusnita Yakob
- Unit of Molecular Diagnostics, Specialised Diagnostics Centre, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Siti Aishah Abdul Wahab
- Unit of Molecular Diagnostics, Specialised Diagnostics Centre, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Ernie Zuraida Ali
- Unit of Inborn Errors of Metabolism and Genetic, Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Mohd Khairul Nizam Mohd Khalid
- Unit of Molecular Diagnostics, Specialised Diagnostics Centre, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Huey-Yin Leong
- Department of Genetics, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586, Kuala Lumpur, Malaysia
| | - Hui-Bein Chew
- Department of Genetics, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586, Kuala Lumpur, Malaysia
| | | | - Lock-Hock Ngu
- Department of Genetics, Hospital Kuala Lumpur, Ministry of Health Malaysia, Jalan Pahang, 50586, Kuala Lumpur, Malaysia
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Nguyen TK, Thuy Thi Tran L, Ho Viet D, Thai PH, Ha TP, Ty PV, Duc LP, Ton That Huu D, Cuong LCV. Xanthine oxidase, α-glucosidase and α-amylase inhibitory activities of the essential oil from Piper lolot: In vitro and in silico studies. Heliyon 2023; 9:e19148. [PMID: 37636421 PMCID: PMC10458695 DOI: 10.1016/j.heliyon.2023.e19148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Piper lolot is a species of herb used as a popular food in Vietnam. Furthermore, the species has been used as a Vietnamese traditional medicine to treat many diseases. Methods Chemical constituents in the essential oil from leaves of Piper lolot were determined using GC/MS analysis. The anti-gout and anti-diabetic activities of the essential oil were determined through the inhibitory assays against xanthine oxidase, α-glucosidase and α-amylase enzymes. In addition, molecular docking simulations were used to elucidate the inhibitory mechanism between the main compounds and the enzymes. Results The dominant constituents of the Piper lolot essential oils were determined as β-caryophyllene (20.6%), β-bisabolene (11.6%), β-selinene (8.4%), β-elemene (7.7%), trans-muurola-4(14),5-diene (7.4%), and (E)-β-ocimene (6.7%). The essential oil displayed xanthine oxidase, α-amylase, and α-glucosidase inhibitory activities with IC50 values of 28.4, 130.6, and 59.1 μg/mL, respectively. The anti-gout and anti-diabetic activities of the essential oil from the P. lolot species are reported for the first time. Furthermore, molecular docking simulation was consistent to in vitro experiments. Conclusion The present study provides initial evidence that the essential oil of P. lolot may be a potential natural source to develop new diabetes preparations.
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Affiliation(s)
- Tan Khanh Nguyen
- Institute of Applied Life Sciences, Dong A University, 33 Xo Viet Nghe Tinh, Hai Chau District, Da Nang, Viet Nam
- Scientific Management Department, Dong A University, Da Nang, Viet Nam
| | - Linh Thuy Thi Tran
- Faculty of Pharmacy, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen, Hue City, Thua Thien Hue, Viet Nam
| | - Duc Ho Viet
- Faculty of Pharmacy, Hue University of Medicine and Pharmacy, Hue University, 06 Ngo Quyen, Hue City, Thua Thien Hue, Viet Nam
| | - Pham Hong Thai
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue, Viet Nam
| | - Tran Phuong Ha
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue, Viet Nam
| | - Pham Viet Ty
- Faculty of Chemistry, University of Education, Hue University, 34 Le Loi, Hue City, Thua Thien Hue, Viet Nam
| | - Le Phu Duc
- Hue Medical College, People's Committee of Thua Thien Hue Province, 01 Nguyen Truong to, Hue City, Thua Thien Hue, Viet Nam
| | - Dat Ton That Huu
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue, Viet Nam
| | - Le Canh Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue, Viet Nam
- Centre for Conservation of Vietnam Natural Resources and Rescue of Animals and Plants, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Phong My, Phong Dien, Thua Thien Hue, Viet Nam
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Fatullayev H, Paşayeva L, Celik I, İnce U, Tugay O. Phytochemical Composition, In Vitro Antimicrobial, Antioxidant, and Enzyme Inhibition Activities, and In Silico Molecular Docking and Dynamics Simulations of Centaurea lycaonica: A Computational and Experimental Approach. ACS OMEGA 2023; 8:22854-22865. [PMID: 37396208 PMCID: PMC10308398 DOI: 10.1021/acsomega.3c01819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023]
Abstract
Centaurea lycaonica is a local endemic species from the Centaurea L. genus. The Centaurea species has a wide range of usage in treating diseases in folk medicine. There are limited biological activity studies on this species in the literature. This study investigated enzyme inhibition and antimicrobial activity, antioxidant effect, and chemical content of extract and fractions of C. lycaonica. Enzyme inhibition activity was tested by α-amylase, α-glucosidase, and tyrosinase enzyme inhibition methods and antimicrobial activity by the microdilution method. The antioxidant activity was investigated using DPPH•, ABTS•+, and FRAP tests. The chemical content was determined by LC-MS/MS. The methanol extract showed the highest activity for α-glucosidase and α-amylase, even surpassing the positive control acarbose, with IC50 values of 56.333 ± 0.986 and 172.800 ± 0.816 μg/mL, respectively. Additionally, the ethyl acetate fraction also exhibited high activity for α-amylase with an IC50 value of 204.067 ± 1.739 μg/mL and tyrosinase with an IC50 value of 213.900 ± 1.553 μg/mL. Moreover, this extract and fraction were found to have the highest total phenolic and flavonoid contents and antioxidant activity. Additionally, LC-MS/MS analyses of active extract and fraction revealed mainly the presence of phenolic compounds and flavonoids. In silico molecular docking and molecular dynamics simulation studies of determining compounds apigenin and myristoleic acid, common in CLM and CLE extracts and active against α-glucosidase and α-amylase, were performed. In conclusion, methanol extract and ethyl acetate fraction showed potential enzyme inhibition and antioxidant activity as a natural agent. Molecular modeling studies corroborate the findings of in vitro activity analyses.
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Affiliation(s)
- Hanifa Fatullayev
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Türkiye
| | - Leyla Paşayeva
- Department
of Pharmacognosy, Faculty of Pharmacy, Erciyes
University, Kayseri 38039, Türkiye
| | - Ismail Celik
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Türkiye
| | - Ufuk İnce
- Department
of Pharmaceutical Microbiology, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Türkiye
| | - Osman Tugay
- Department
of Pharmaceutical Botany, Faculty of Pharmacy, Selçuk University, Konya 42130, Türkiye
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Safapoor S, Halimi M, Ghomi MK, Noori M, Dastyafteh N, Javanshir S, Hosseini S, Mojtabavi S, Faramarzi MA, Nasli-Esfahani E, Larijani B, Fakhrioliaei A, Dekamin MG, Mohammadi-Khanaposhtani M, Mahdavi M. Synthesis, ADMT prediction, and in vitro and in silico α-glucosidase inhibition evaluations of new quinoline-quinazolinone-thioacetamides. RSC Adv 2023; 13:19243-19256. [PMID: 37377867 PMCID: PMC10291282 DOI: 10.1039/d3ra01790g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
In this work, a new series of quinoline-quinazolinone-thioacetamide derivatives 9a-p were designed using a combination of effective pharmacophores of the potent α-glucosidase inhibitors. These compounds were synthesized by simple chemical reactions and evaluated for their anti-α-glucosidase activity. Among the tested compounds, compounds 9a, 9f, 9g, 9j, 9k, and 9m demonstrated significant inhibition effects in comparison to the positive control acarbose. Particularly, compound 9g with inhibitory activity around 83-fold more than acarbose exhibited the best anti-α-glucosidase activity. Compound 9g showed a competitive type of inhibition in the kinetic study, and the molecular simulation studies demonstrated that this compound with a favorable binding energy occupied the active site of α-glucosidase. Furthermore, in silico ADMET studies of the most potent compounds 9g, 9a, and 9f were performed to predict their drug-likeness, pharmacokinetic, and toxicity properties.
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Affiliation(s)
- Sajedeh Safapoor
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences Tehran Iran
| | - Mohammad Halimi
- Department of Biology, Islamic Azad University Babol Branch Babol Iran
| | - Minoo Khalili Ghomi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences Tehran Iran
| | - Milad Noori
- Pharmaceutical and Heterocyclic Chemistry Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran
| | - Navid Dastyafteh
- Pharmaceutical and Heterocyclic Chemistry Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran
| | - Shahrzad Javanshir
- Pharmaceutical and Heterocyclic Chemistry Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran
| | | | - Somayeh Mojtabavi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences Tehran Iran
| | - Mohammad Ali Faramarzi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences Tehran Iran
| | - Ensieh Nasli-Esfahani
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences Tehran Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences Tehran Iran
| | - Azadeh Fakhrioliaei
- Faculty of Pharmacy, Islamic Azad University Pharmaceutical Sciences Branch Tehran Iran
| | - Mohammad G Dekamin
- Pharmaceutical and Heterocyclic Chemistry Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran
| | - Maryam Mohammadi-Khanaposhtani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences Babol Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences Tehran Iran
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Sahasrabudhe SA, Terluk MR, Kartha RV. N-acetylcysteine Pharmacology and Applications in Rare Diseases-Repurposing an Old Antioxidant. Antioxidants (Basel) 2023; 12:1316. [PMID: 37507857 PMCID: PMC10376274 DOI: 10.3390/antiox12071316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 07/30/2023] Open
Abstract
N-acetylcysteine (NAC), a precursor of cysteine and, thereby, glutathione (GSH), acts as an antioxidant through a variety of mechanisms, including oxidant scavenging, GSH replenishment, antioxidant signaling, etc. Owing to the variety of proposed targets, NAC has a long history of use as a prescription product and in wide-ranging applications that are off-label as an over-the-counter (OTC) product. Despite its discovery in the early 1960s and its development for various indications, systematic clinical pharmacology explorations of NAC pharmacokinetics (PK), pharmacodynamic targets, drug interactions, and dose-ranging are sorely limited. Although there are anecdotal instances of NAC benefits in a variety of diseases, a comprehensive review of the use of NAC in rare diseases does not exist. In this review, we attempt to summarize the existing literature focused on NAC explorations in rare diseases targeting mitochondrial dysfunction along with the history of NAC usage, approved indications, mechanisms of action, safety, and PK characterization. Further, we introduce the research currently underway on other structural derivatives of NAC and acknowledge the continuum of efforts through pre-clinical and clinical research to facilitate further therapeutic development of NAC or its derivatives for rare diseases.
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Affiliation(s)
- Siddhee A Sahasrabudhe
- Center for Orphan Drug Research, Department of Experimental and Clinical Pharmacology, Rm 4-214, McGuire Translational Research Facility, 2001 6th St. SE, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Marcia R Terluk
- Center for Orphan Drug Research, Department of Experimental and Clinical Pharmacology, Rm 4-214, McGuire Translational Research Facility, 2001 6th St. SE, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reena V Kartha
- Center for Orphan Drug Research, Department of Experimental and Clinical Pharmacology, Rm 4-214, McGuire Translational Research Facility, 2001 6th St. SE, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
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Fu Y, Liu Z, Wang H, Zhang F, Guo S, Shen Q. Comparison of the generation of α-glucosidase inhibitory peptides derived from prolamins of raw and cooked foxtail millet: In vitro activity, de novo sequencing, and in silico docking. Food Chem 2023; 411:135378. [PMID: 36669338 DOI: 10.1016/j.foodchem.2022.135378] [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: 10/13/2022] [Revised: 12/15/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023]
Abstract
Foxtail millet prolamin has been demonstrated to have anti-diabetic effects. In this study, we compared the generation of anti-α-glucosidase peptides derived from prolamins of raw and cooked foxtail millet (PRFM and PCFM). PRFM and PCFM hydrolysates (PRFMH and PCFMH) both exhibited α-glucosidase inhibitory activity. After ultrafiltration according to molecular weight (Mw), the fraction with Mw < 3 kDa in PCFMH (PCFMH<3) showed higher α-glucosidase inhibitory activity than that in PRFMH (PRFMH<3). The composition of α-glucosidase inhibitory peptides identified by de novo sequencing in PCFMH<3 and PRFMH<3 was compared by virtual screening, combining biological activity, net charge, grand average of hydropathicity (GRAVY), and key hydrophobic amino acids (Met, Pro, Phe, and Leu). We found that the proportion of peptides with excellent α-glucosidase binding force in PCFMH<3 was higher than in PRFMH<3. Overall, cooking may positively affect the generation of peptides that perform well in inhibiting α-glucosidase derived from foxtail millet prolamin.
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Affiliation(s)
- Yongxia Fu
- Shanxi Institute for Functional Food, Shanxi Agricultural University, Taiyuan, China; National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, National Engineering Research Center for Fruit and Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhenyu Liu
- National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, National Engineering Research Center for Fruit and Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Han Wang
- National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, National Engineering Research Center for Fruit and Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fan Zhang
- National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, National Engineering Research Center for Fruit and Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Industrial Technology Research Institute Ltd, Beijing, China
| | - Shang Guo
- Shanxi Institute for Functional Food, Shanxi Agricultural University, Taiyuan, China
| | - Qun Shen
- National Center of Technology Innovation (Deep Processing of Highland Barley) in Food Industry, National Engineering Research Center for Fruit and Vegetable Processing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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Rashid RSM, Temurlu S, Abourajab A, Karsili P, Dinleyici M, Al-Khateeb B, Icil H. Drug Repurposing of FDA Compounds against α-Glucosidase for the Treatment of Type 2 Diabetes: Insights from Molecular Docking and Molecular Dynamics Simulations. Pharmaceuticals (Basel) 2023; 16:ph16040555. [PMID: 37111312 PMCID: PMC10145898 DOI: 10.3390/ph16040555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Type 2 diabetes mellitus is a chronic health problem that can be controlled by slowing one's carbohydrate metabolism by inhibiting α-glucosidase, an enzyme responsible for carbohydrate degradation. Currently, drugs for type 2 diabetes have limitations in terms of safety, efficiency, and potency, while cases are rapidly increasing. For this reason, the study planned and moved towards drug repurposing by utilizing food and drug administration (FDA)-approved drugs against α-glucosidase, and investigated the molecular mechanisms. The target protein was refined and optimized by introducing missing residues, and minimized to remove clashes to find the potential inhibitor against α-glucosidase. The most active compounds were selected after the docking study to generate a pharmacophore query for the virtual screening of FDA-approved drug molecules based on shape similarity. The analysis was performed using Autodock Vina (ADV)-based on binding affinities (-8.8 kcal/mol and -8.6 kcal/mol) and root-mean-square-deviation (RMSD) values (0.4 Å and 0.6 Å). Two of the most potent lead compounds were selected for a molecular dynamics (MD) simulation to determine the stability and specific interactions between receptor and ligand. The docking score, RMSD values, pharmacophore studies, and MD simulations revealed that two compounds, namely Trabectedin (ZINC000150338708) and Demeclocycline (ZINC000100036924), are potential inhibitors for α-glucosidase compared to standard inhibitors. These predictions showed that the FDA-approved molecules Trabectedin and Demeclocycline are potential suitable candidates for repurposing against type 2 diabetes. The in vitro studies showed that trabectedin was significantly effective with an IC50 of 1.263 ± 0.7 μM. Further investigation in the laboratory is needed to justify the safety of the drug to be used in vivo.
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Affiliation(s)
- Rebwar Saeed M Rashid
- Department of Chemistry, Faculty of Arts and Science, Eastern Mediterranean University, Famagusta 99628, Northern Cyprus, Mersin 10, Turkey
- Department of Chemistry, Faculty of Education, University of Sulaimani, Sulaymaniyah 46001, Iraq
| | - Selin Temurlu
- Department of Chemistry, Faculty of Arts and Science, Eastern Mediterranean University, Famagusta 99628, Northern Cyprus, Mersin 10, Turkey
| | - Arwa Abourajab
- Department of Chemistry, Faculty of Arts and Science, Eastern Mediterranean University, Famagusta 99628, Northern Cyprus, Mersin 10, Turkey
| | - Pelin Karsili
- Department of Chemistry, Faculty of Arts and Science, Eastern Mediterranean University, Famagusta 99628, Northern Cyprus, Mersin 10, Turkey
| | - Meltem Dinleyici
- Department of Chemistry, Faculty of Arts and Science, Eastern Mediterranean University, Famagusta 99628, Northern Cyprus, Mersin 10, Turkey
| | - Basma Al-Khateeb
- Department of Chemistry, Faculty of Arts and Science, Eastern Mediterranean University, Famagusta 99628, Northern Cyprus, Mersin 10, Turkey
| | - Huriye Icil
- Department of Chemistry, Faculty of Arts and Science, Eastern Mediterranean University, Famagusta 99628, Northern Cyprus, Mersin 10, Turkey
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Saddik R, Brandán SA, Mortada S, Baydere C, Roby O, Dege N, Tighadouini S, Tahiri M, Faouzi MA, Karrouchi K. Synthesis, crystal structure, Hirshfeld surface analysis, DFT and antihyperglycemic activity of 9-allyl-2,3,9,10a-tetrahydrobenzo[b]cyclopenta[e][1,4]diazepin-10(1H)-one. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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41
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High-specific activity variants of recombinant human α-glucosidase for the treatment of Pompe disease. Med Hypotheses 2023. [DOI: 10.1016/j.mehy.2023.111044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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Arumapperuma T, Li J, Hornung B, Soler NM, Goddard-Borger ED, Terrapon N, Williams SJ. A subfamily classification to choreograph the diverse activities within glycoside hydrolase family 31. J Biol Chem 2023; 299:103038. [PMID: 36806678 PMCID: PMC10074150 DOI: 10.1016/j.jbc.2023.103038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The Carbohydrate-Active Enzyme classification groups enzymes that breakdown, assemble, or decorate glycans into protein families based on sequence similarity. The glycoside hydrolases (GH) are arranged into over 170 enzyme families, with some being very large and exhibiting distinct activities/specificities towards diverse substrates. Family GH31 is a large family that contains more than 20,000 sequences with a wide taxonomic diversity. Less than 1% of GH31 members are biochemically characterized and exhibit many different activities that include glycosidases, lyases, and transglycosidases. This diversity of activities limits our ability to predict the activities and roles of GH31 family members in their host organism and our ability to exploit these enzymes for practical purposes. Here, we established a subfamily classification using sequence similarity networks that was further validated by a structural analysis. While sequence similarity networks provide a sequence-based separation, we obtained good segregation between activities among the subfamilies. Our subclassification consists of 20 subfamilies with sixteen subfamilies containing at least one characterized member and eleven subfamilies that are monofunctional based on the available data. We also report the biochemical characterization of a member of the large subfamily 2 (GH31_2) that lacked any characterized members: RaGH31 from Rhodoferax aquaticus is an α-glucosidase with activity on a range of disaccharides including sucrose, trehalose, maltose, and nigerose. Our subclassification provides improved predictive power for the vast majority of uncharacterized proteins in family GH31 and highlights the remaining sequence space that remains to be functionally explored.
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Affiliation(s)
- Thimali Arumapperuma
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Jinling Li
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Bastian Hornung
- AFMB, UMR 7257 CNRS Aix-Marseille Univ., USC 1408 INRAE, Marseille, France
| | - Niccolay Madiedo Soler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Nicolas Terrapon
- AFMB, UMR 7257 CNRS Aix-Marseille Univ., USC 1408 INRAE, Marseille, France
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria, Australia.
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Acar Çevik U, Celik I, Paşayeva L, Fatullayev H, Bostancı HE, Özkay Y, Kaplancıklı ZA. New benzimidazole-oxadiazole derivatives: Synthesis, α-glucosidase, α-amylase activity, and molecular modeling studies as potential antidiabetic agents. Arch Pharm (Weinheim) 2023; 356:e2200663. [PMID: 36760015 DOI: 10.1002/ardp.202200663] [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: 12/19/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/11/2023]
Abstract
Benzimidazole-1,3,4-oxadiazole derivatives (5a-z) were synthesized and characterized with different spectroscopic techniques such as 1 H NMR, 13 C NMR, and HRMS. The synthesized analogs were examined against α-glucosidase and α-amylase enzymes to determine their antidiabetic potential. Compounds 5g and 5q showed the most activity with 35.04 ± 1.28 and 47.60 ± 2.16 µg/mL when compared with the reference drug acarbose (IC50 = 54.63 ± 1.95 µg/mL). Compounds 5g, 5o, 5s, and 5x were screened against the α-amylase enzyme and were found to show excellent potential, with IC50 values ranging from 22.39 ± 1.40 to 32.07 ± 1.55 µg/mL, when compared with the standard acarbose (IC50 = 46.21 ± 1.49 µg/mL). The antioxidant activities of the effective compounds (5o, 5g, 5s, 5x, and 5q) were evaluated by TAS methods. A molecular docking research study was conducted to identify the active site and explain the functions of the active chemicals. To investigate the most likely binding mode of the substances 5g, 5o, 5q, 5s, and 5x, a molecular dynamics simulation was also carried out.
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Affiliation(s)
- Ulviye Acar Çevik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Leyla Paşayeva
- Department of Pharmacognosy, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Hanifa Fatullayev
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Hayrani E Bostancı
- Department of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - Yusuf Özkay
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Zafer A Kaplancıklı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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Lin HY, Chang SY, Teng HH, Wu HJ, Li HY, Cheng CC, Chuang CK, Lin HY, Lin SP, Cheng WC. Discovery of small-molecule protein stabilizers toward exogenous alpha-l-iduronidase to reduce the accumulated heparan sulfate in mucopolysaccharidosis type I cells. Eur J Med Chem 2023; 247:115005. [PMID: 36563498 DOI: 10.1016/j.ejmech.2022.115005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/16/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022]
Abstract
Synthesis of a series of l-iduronic acid (IdoA)- and imino-IdoA-typed C-glycosides for modulating α-l-iduronidase (IDUA) activity is described. In an enzyme inhibition study, IdoA-typed C-glycosides were more potent than imino-IdoA analogs, with the most potent IdoA-typed C-glycoside 27c showing an IC50 value of 1 μM. On the other hand, co-treatment of 12 with rh-α-IDUA in mucopolysaccharidosis type I (MPS I) fibroblasts exhibited a nearly 3-fold increase of the IDUA activity, resulting in a clear reduction of the accumulated heparan sulfate (HS) compared to the exogenous enzyme treatment alone. This is the first report of small molecules facilitating IDUA stabilization, enhancing enzyme activity, and reducing accumulated HS in MPS I cell-based assays, which reveals that small molecules as rh-α-IDUA stabilizers to improve enzyme replacement therapy (ERT) efficacy toward MPS I is feasible and promising.
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Affiliation(s)
- Hung-Yi Lin
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Shih-Ying Chang
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Hsuan-Hsuan Teng
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Hsi-Ju Wu
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Huang-Yi Li
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Chia-Chun Cheng
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Chih-Kuang Chuang
- Department of Medical Research, MacKay Memorial Hospital, Tamsui District, New Taipei City, 25160, Taiwan
| | - Hsiang-Yu Lin
- Department of Medical Research, MacKay Memorial Hospital, Tamsui District, New Taipei City, 25160, Taiwan; Department of Pediatrics and Rare Disease Center, MacKay Memorial Hospital, Taipei, 10449, Taiwan
| | - Shuan-Pei Lin
- Department of Medical Research, MacKay Memorial Hospital, Tamsui District, New Taipei City, 25160, Taiwan; Department of Pediatrics and Rare Disease Center, MacKay Memorial Hospital, Taipei, 10449, Taiwan
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 115, Taiwan; Department of Chemistry, National Cheng Kung University, Tainan City, 701, Taiwan.
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Identification of promising multi-targeting inhibitors of obesity from Vernonia amygdalina through computational analysis. Mol Divers 2023; 27:1-25. [PMID: 35179699 DOI: 10.1007/s11030-022-10397-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023]
Abstract
Vernonia amygdalina, a widely consumed West African food herb, can be a boon in the discovery of safe anti-obesity agents given the extensive reports on its anti-obesity and antidiabetic potentials. The main aim of this study was to screen 78 Vernonia-Derived Phytocompounds (VDPs) against the active site regions of Human Pancreatic Lipase (HPL), Human Pancreatic Amylase and Human Glucosidase (HG) as drug targets associated with obesity in silico. Structure-based virtual screening helped to identify Luteolin 7-O-glucuronoside and Andrographidoid D2 as hit compounds with dual targeting tendency towards the HPL and HG. Analysis of the molecular dynamic simulation trajectory files of the ligand-receptor complexes as computed from the thermodynamic parameters plots showed not only increased flexibility and greater interaction potential of the active site residues of the receptor towards the VDPs as indicated by the root mean square fluctuation but also higher stability as indicated by the root mean square deviation, radius of gyration and number of hydrogen bonds. The cluster analysis further showed that the interactions with important residues were preserved in the dynamic environment. These observations were further verified from Molecular Mechanics Generalized Born Surface Area Analysis, which also showed that residual contributions to the binding free energies were mainly from catalytic residues at the active sites of the enzymes. The hit compounds also feature desirable physicochemical properties and drug-likeness. This study provides in silico evidence for the inhibitory potential of phytochemicals from Vernonia amygdalina against two target enzymes in obesity.
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Synthesis, Molecular Docking, and Bioactivity Study of Novel Hybrid Benzimidazole Urea Derivatives: A Promising α-Amylase and α-Glucosidase Inhibitor Candidate with Antioxidant Activity. Pharmaceutics 2023; 15:pharmaceutics15020457. [PMID: 36839780 PMCID: PMC9963656 DOI: 10.3390/pharmaceutics15020457] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
A novel series of benzimidazole ureas 3a-h were elaborated using 2-(1H-benzoimidazol-2-yl) aniline 1 and the appropriate isocyanates 2a-h. The antioxidant and possible antidiabetic activities of the target benzimidazole-ureas 3a-h were evaluated. Almost all compounds 3a-h displayed strong to moderate antioxidant activities. When tested using the three antioxidant techniques, TAC, FRAP, and MCA, compounds 3b and 3c exhibited marked activity. The most active antioxidant compound in this family was compound 3g, which had excellent activity using four different methods: TAC, FRAP, DPPH-SA, and MCA. In vitro antidiabetic assays against α-amylase and α-glucosidase enzymes revealed that the majority of the compounds tested had good to moderate activity. The most favorable results were obtained with compounds 3c, 3e, and 3g, and analysis revealed that compounds 3c (IC50 = 18.65 ± 0.23 μM), 3e (IC50 = 20.7 ± 0.06 μM), and 3g (IC50 = 22.33 ± 0.12 μM) had good α-amylase inhibitory potential comparable to standard acarbose (IC50 = 14.21 ± 0.06 μM). Furthermore, the inhibitory effect of 3c (IC50 = 17.47 ± 0.03 μM), 3e (IC50 = 21.97 ± 0.19 μM), and 3g (IC50 = 23.01 ± 0.12 μM) on α-glucosidase was also comparable to acarbose (IC50 = 15.41 ± 0.32 μM). According to in silico molecular docking studies, compounds 3a-h had considerable affinity for the active sites of human lysosomal acid α-glucosidase (HLAG) and pancreatic α-amylase (HPA), indicating that the majority of the examined compounds had potential anti-hyperglycemic action.
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4-Methylumbelliferone Targets Revealed by Public Data Analysis and Liver Transcriptome Sequencing. Int J Mol Sci 2023; 24:ijms24032129. [PMID: 36768453 PMCID: PMC9917189 DOI: 10.3390/ijms24032129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
4-methylumbelliferone (4MU) is a well-known hyaluronic acid synthesis inhibitor and an approved drug for the treatment of cholestasis. In animal models, 4MU decreases inflammation, reduces fibrosis, and lowers body weight, serum cholesterol, and insulin resistance. It also inhibits tumor progression and metastasis. The broad spectrum of effects suggests multiple and yet unknown targets of 4MU. Aiming at 4MU target deconvolution, we have analyzed publicly available data bases, including: 1. Small molecule library Bio Assay screening (PubChemBioAssay); 2. GO pathway databases screening; 3. Protein Atlas Database. We also performed comparative liver transcriptome analysis of mice on normal diet and mice fed with 4MU for two weeks. Potential targets of 4MU public data base analysis fall into two big groups, enzymes and transcription factors (TFs), including 13 members of the nuclear receptor superfamily regulating lipid and carbohydrate metabolism. Transcriptome analysis revealed changes in the expression of genes involved in bile acid metabolism, gluconeogenesis, and immune response. It was found that 4MU feeding decreased the accumulation of the glycogen granules in the liver. Thus, 4MU has multiple targets and can regulate cell metabolism by modulating signaling via nuclear receptors.
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Li HY, Lee NC, Chiu YT, Chang YW, Lin CC, Chou CL, Chien YH, Hwu WL, Cheng WC. Harnessing polyhydroxylated pyrrolidines as a stabilizer of acid alpha-glucosidase (GAA) to enhance the efficacy of enzyme replacement therapy in Pompe disease. Bioorg Med Chem 2023; 78:117129. [PMID: 36542959 DOI: 10.1016/j.bmc.2022.117129] [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: 10/17/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
To discover small molecules as acid alpha-glucosidase (GAA) stabilizers for potential benefits of the exogenous enzyme treatment toward Pompe disease cells, we started from the initial screening of the unique chemical space, consisting of sixteen stereoisomers of 2-aminomethyl polyhydroxylated pyrrolidines (ADMDPs) to find out two primary stabilizers 17 and 18. Further external or internal structural modifications of 17 and 18 were performed to increase structural diversity, followed by the protein thermal shift study to evaluate the GAA stabilizing ability. Fortunately, pyrrolidine 21, possessing an l-arabino-typed configuration pattern, was identified as a specific potent rh-GAA stabilizer, enabling the suppression of rh-GAA protein denaturation. In a cell-based Pompe model, co-administration of 21 with rh-GAA protein significantly improved enzymatic activity (up to 5-fold) compared to administration of enzyme alone. Potentially, pyrrolidine 21 enables the direct increase of ERT (enzyme replacement therapy) efficacy in cellulo and in vivo.
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Affiliation(s)
- Huang-Yi Li
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, 1001, University Road, Hsinchu 300, Taiwan
| | - Ni-Chung Lee
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan
| | - Yu-Ting Chiu
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yu-Wen Chang
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chu-Chung Lin
- AnHorn Medicines Co., Ltd. National Biotechnology Research Park C522, 99, Lane 130, Academia Road, Section 1, Nankang, Taipei 11529, Taiwan
| | - Cheng-Li Chou
- AnHorn Medicines Co., Ltd. National Biotechnology Research Park C522, 99, Lane 130, Academia Road, Section 1, Nankang, Taipei 11529, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan.
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Department of Chemistry, National Cheng Kung University, 1, University Road, Tainan 70101, Taiwan; Department of Chemistry, National University of Kaohsiung, 700, Kaohsiung University Road, Nanzih District, Kaohsiung 81148, Taiwan; Department of Chemistry, National Chiayi University, 300, Syuefu Road, Chiayi 60004, Taiwan.
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Synthesis, crystal structures, spectroscopic characterization and in vitro evaluation of the 4-sulfono-3-methoxycinnamaldehydes as potential α-glucosidase and/or α-amylase inhibitors. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Isolation of a Novel Anti-Diabetic α-Glucosidase Oligo-Peptide Inhibitor from Fermented Rice Bran. Foods 2023; 12:foods12010183. [PMID: 36613397 PMCID: PMC9818066 DOI: 10.3390/foods12010183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
At present, the incidence rate of diabetes is increasing gradually, and inhibiting α-glucosidase is one of the effective methods used to control blood sugar. This study identified new peptides from rice bran fermentation broth and evaluated their inhibitory activity and mechanism against α-glucosidase. Rice bran was fermented with Bacillus subtilis MK15 and the polypeptides of <3 kDa were isolated by ultrafiltration and chromatographic column, and were then subjected to LC-MS/MS mass spectrometry analysis. The results revealed that the oligopeptide GLLGY showed the greatest inhibitory activity in vitro. Docking studies with GLLGY on human α-glucosidase (PDB ID 5NN8) suggested a binding energy of −7.1 kcal/mol. GLLGY acts as a non-competitive inhibitor and forms five hydrogen bonds with Asp282, Ser523, Asp616, and His674 of α-glucosidase. Moreover, it retained its inhibitory activity even in a simulated digestion environment in vitro. The oligopeptide GLLGY could be developed into a potential anti-diabetic agent.
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