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Chen Y, Fan Z, Luo Z, Kang X, Wan R, Li F, Lin W, Han Z, Qi B, Lin J, Sun Y, Huang J, Xu Y, Chen S. Impacts of Nutlin-3a and exercise on murine double minute 2-enriched glioma treatment. Neural Regen Res 2025; 20:1135-1152. [PMID: 38989952 DOI: 10.4103/nrr.nrr-d-23-00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 12/21/2023] [Indexed: 07/12/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202504000-00029/figure1/v/2024-07-06T104127Z/r/image-tiff Recent research has demonstrated the impact of physical activity on the prognosis of glioma patients, with evidence suggesting exercise may reduce mortality risks and aid neural regeneration. The role of the small ubiquitin-like modifier (SUMO) protein, especially post-exercise, in cancer progression, is gaining attention, as are the potential anti-cancer effects of SUMOylation. We used machine learning to create the exercise and SUMO-related gene signature (ESLRS). This signature shows how physical activity might help improve the outlook for low-grade glioma and other cancers. We demonstrated the prognostic and immunotherapeutic significance of ESLRS markers, specifically highlighting how murine double minute 2 (MDM2), a component of the ESLRS, can be targeted by nutlin-3. This underscores the intricate relationship between natural compounds such as nutlin-3 and immune regulation. Using comprehensive CRISPR screening, we validated the effects of specific ESLRS genes on low-grade glioma progression. We also revealed insights into the effectiveness of Nutlin-3a as a potent MDM2 inhibitor through molecular docking and dynamic simulation. Nutlin-3a inhibited glioma cell proliferation and activated the p53 pathway. Its efficacy decreased with MDM2 overexpression, and this was reversed by Nutlin-3a or exercise. Experiments using a low-grade glioma mouse model highlighted the effect of physical activity on oxidative stress and molecular pathway regulation. Notably, both physical exercise and Nutlin-3a administration improved physical function in mice bearing tumors derived from MDM2-overexpressing cells. These results suggest the potential for Nutlin-3a, an MDM2 inhibitor, with physical exercise as a therapeutic approach for glioma management. Our research also supports the use of natural products for therapy and sheds light on the interaction of exercise, natural products, and immune regulation in cancer treatment.
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Affiliation(s)
- Yisheng Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhongcheng Fan
- Department of Orthopedic Surgery, Hainan Province Clinical Medical Center, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, Hainan Province, China
| | - Zhiwen Luo
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xueran Kang
- Department of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renwen Wan
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangqi Li
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Weiwei Lin
- Department of Neurosurgery, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhihua Han
- Department of Orthopedics, Shanghai General Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, China
| | - Beijie Qi
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinrong Lin
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yaying Sun
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiebin Huang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Shiyi Chen
- Department of Sport Medicine, Huashan Hospital, Fudan University, Shanghai, China
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Marasco M, Kirkpatrick J, Carlomagno T, Hub JS, Anselmi M. Phosphopeptide binding to the N-SH2 domain of tyrosine phosphatase SHP2 correlates with the unzipping of its central β-sheet. Comput Struct Biotechnol J 2024; 23:1169-1180. [PMID: 38510972 PMCID: PMC10951427 DOI: 10.1016/j.csbj.2024.02.023] [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: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
SHP2 is a tyrosine phosphatase that plays a regulatory role in multiple intracellular signaling cascades and is known to be oncogenic in certain contexts. In the absence of effectors, SHP2 adopts an autoinhibited conformation with its N-SH2 domain blocking the active site. Given the key role of N-SH2 in regulating SHP2, this domain has been extensively studied, often by X-ray crystallography. Using a combination of structural analyses and molecular dynamics (MD) simulations we show that the crystallographic environment can significantly influence the structure of the isolated N-SH2 domain, resulting in misleading interpretations. As an orthogonal method to X-ray crystallography, we use a combination of NMR spectroscopy and MD simulations to accurately determine the conformation of apo N-SH2 in solution. In contrast to earlier reports based on crystallographic data, our results indicate that apo N-SH2 in solution primarily adopts a conformation with a fully zipped central β-sheet, and that partial unzipping of this β-sheet is promoted by binding of either phosphopeptides or even phosphate/sulfate ions.
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Affiliation(s)
- Michelangelo Marasco
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Kirkpatrick
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Teresa Carlomagno
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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Liao Y, Cao P, Luo L. Development of novel ALOX15 inhibitors combining dual machine learning filtering and fragment substitution optimisation approaches, molecular docking and dynamic simulation methods. J Enzyme Inhib Med Chem 2024; 39:2301756. [PMID: 38213304 PMCID: PMC10791093 DOI: 10.1080/14756366.2024.2301756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024] Open
Abstract
The oxidation of unsaturated lipids, facilitated by the enzyme Arachidonic acid 15-lipoxygenase (ALOX15), is an essential element in the development of ferroptosis. This study combined a dual-score exclusion strategy with high-throughput virtual screening, naive Bayesian and recursive partitioning machine learning models, the already established ALOX15 inhibitor i472, and a docking-based fragment substitution optimisation approach to identify potential ALOX15 inhibitors, ultimately leading to the discovery of three FDA-approved drugs that demonstrate optimal inhibitory potential against ALOX15. Through fragment substitution-based optimisation, seven new inhibitor structures have been developed. To evaluate their practicality, ADMET predictions and molecular dynamics simulations were performed. In conclusion, the compounds found in this study provide a novel approach to combat conditions related to ferroptosis-related injury by inhibiting ALOX15.
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Affiliation(s)
- Yinglin Liao
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Peng Cao
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
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4
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Pham C, Stogios PJ, Savchenko A, Mahadevan R. Computation-guided transcription factor biosensor specificity engineering for adipic acid detection. Comput Struct Biotechnol J 2024; 23:2211-2219. [PMID: 38817964 PMCID: PMC11137364 DOI: 10.1016/j.csbj.2024.05.002] [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: 12/13/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
Transcription factor (TF)-based biosensors that connect small-molecule sensing with readouts such as fluorescence have proven to be useful synthetic biology tools for applications in biotechnology. However, the development of specific TF-based biosensors is hindered by the limited repertoire of TFs specific for molecules of interest since current construction methods rely on a limited set of characterized TFs. In this study, we present an approach for engineering the specificity of TFs through a computation-based workflow using molecular docking that enables targeted alteration of TF ligand specificity. Using this method, we engineer the LysR family BenM TF to alter its specificity from its cognate ligand cis,cis-muconic acid to adipic acid through a single amino acid substitution identified by our computational workflow. When implemented in a cell-free system, the engineered biosensor shows higher ligand sensitivity, expanding the potential applications of this circuit. We further investigate ligand binding through molecular dynamics to analyze the substitution, elucidating the impact of modulating a single amino acid position on the mechanism of BenM ligand binding. This study represents the first application of biomolecular modeling methods for altering BenM specificity and for gaining insights into how mutations influence the structural dynamics of BenM. Such methods can potentially be applied to other TFs to alter specificity and analyze the dynamics responsible for these changes, highlighting the applicability of computational tools for informing experiments. In addition, our developed adipic acid biosensor can be applied for the identification and engineering of enzymes to produce adipic acid.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
- The Institute of Biomedical Engineering, University of Toronto, Ontario, Canada
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Li Q, Zhou SR, Kim H, Wang H, Zhu JJ, Yang JK. Discovering novel Cathepsin L inhibitors from natural products using artificial intelligence. Comput Struct Biotechnol J 2024; 23:2606-2614. [PMID: 39006920 PMCID: PMC11245987 DOI: 10.1016/j.csbj.2024.06.009] [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: 02/05/2024] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 07/16/2024] Open
Abstract
Cathepsin L (CTSL) is a promising therapeutic target for metabolic disorders. Current pharmacological interventions targeting CTSL have demonstrated potential in reducing body weight gain, serum insulin levels, and improving glucose tolerance. However, the clinical application of CTSL inhibitors remains limited. In this study, we used a combination of artificial intelligence and experimental methods to identify new CTSL inhibitors from natural products. Through a robust deep learning model and molecular docking, we screened 150 molecules from natural products for experimental validation. At a concentration of 100 µM, we found that 36 of them exhibited more than 50 % inhibition of CTSL. Notably, 13 molecules displayed over 90 % inhibition and exhibiting concentration-dependent effects. The molecular dynamics simulation on the two most potent inhibitors, Plumbagin and Beta-Lapachone, demonstrated stable interaction at the CTSL active site. Enzyme kinetics studies have shown that these inhibitors exert an uncompetitive inhibitory effect on CTSL. In conclusion, our research identifies Plumbagin and Beta-Lapachone as potential CTSL inhibitors, offering promising candidates for the treatment of metabolic disorders and illustrating the effectiveness of artificial intelligence in drug discovery.
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Affiliation(s)
- Qi Li
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Si-Rui Zhou
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Hanna Kim
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Hao Wang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Juan-Juan Zhu
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
| | - Jin-Kui Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China
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Fan S, Lü X, Wei X, Lü R, Feng C, Jin Y, Yan M, Yang Z. Computational design of α-amylase from Bacillus licheniformis to increase its activity and stability at high temperatures. Comput Struct Biotechnol J 2024; 23:982-989. [PMID: 38404709 PMCID: PMC10883975 DOI: 10.1016/j.csbj.2024.02.005] [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: 09/12/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/27/2024] Open
Abstract
The thermostable α-amylase derived from Bacillus licheniformis (BLA) has multiple advantages, including enhancing the mass transfer rate and by reducing microbial contamination in starch hydrolysis. Nonetheless, the application of BLA is constrained by the accessibility and stability of enzymes capable of achieving high conversion rates at elevated temperatures. Moreover, the thermotolerance of BLA requires further enhancement. Here, we developed a computational strategy for constructing small and smart mutant libraries to identify variants with enhanced thermostability. Initially, molecular dynamics (MD) simulations were employed to identify the regions with high flexibility. Subsequently, FoldX, a computational design predictor, was used to design mutants by rigidifying highly flexible residues, whereas the simultaneous decrease in folding free energy assisted in improving thermostability. Through the utilization of MD and FoldX, residues K251, T277, N278, K319, and E336, situated at a distance of 5 Å from the catalytic triad, were chosen for mutation. Seventeen mutants were identified and characterized by evaluating enzymatic characteristics and kinetic parameters. The catalytic efficiency of the E271L/N278K mutant reached 184.1 g L-1 s-1, which is 1.88-fold larger than the corresponding value determined for the WT. Furthermore, the most thermostable mutant, E336S, exhibited a 1.43-fold improvement in half-life at 95 ℃, compared with that of the WT. This study, by combining computational simulation with experimental verification, establishes that potential sites can be computationally predicted to increase the activity and stability of BLA and thus provide a possible strategy by which to guide protein design.
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Affiliation(s)
- Shuai Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xudong Lü
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiyu Wei
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ruijie Lü
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Cuiyue Feng
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yuanyuan Jin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao 276800, Shandong, China
| | - Zhaoyong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Tang L, Wang D, Chang H, Liu Z, Zhang X, Feng X, Han L. Treating ischemic stroke by improving vascular structure and promoting angiogenesis using Taohong Siwu Decoction: An integrative pharmacology strategy. JOURNAL OF ETHNOPHARMACOLOGY 2024; 332:118372. [PMID: 38777084 DOI: 10.1016/j.jep.2024.118372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Neovessels represent a crucial therapeutic target and strategy for repairing ischemic tissue. Taohong Siwu Decoction (THSWD) exhibits potential in promoting angiogenesis to address ischemic stroke (IS). However, its impact on neovessel structure and function, alongside the underlying molecular mechanisms, remains elusive. AIM OF THE STUDY Our aim is to investigate the protective effects of THSWD on neovessel structure and function, as well as the associated molecular mechanisms, utilizing an integrative pharmacological approach. MATERIALS AND METHODS We initially employed behavioral tests, 2,3,5-triphenyltetrazolium chloride (TTC) staining, Haematoxylin-eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), Laser Doppler flowmetry (LDF), Evans blue staining, and immunofluorescence to evaluate the protective effects of THSWD on neovascular structure and function in middle cerebral artery occlusion/reperfusion (MCAO/R) rats. Subsequently, we utilized network pharmacology, metabolomics, and experimental validation to elucidate the underlying molecular mechanisms of THSWD in enhancing neovascular structure and function. RESULT In addition to significantly reducing neurological deficits and cerebral infarct volume, THSWD mitigated pathological damage, blood-brain barrier (BBB) leakage, and cerebral blood flow disruption. Moreover, it preserved neovascular structure and stimulated angiogenesis. THSWD demonstrated potential in ameliorating cerebral microvascular metabolic disturbances including lipoic acid metabolism, fructose and mannose metabolism, purine metabolism, and ether lipid metabolism. Consequently, it exhibited multifaceted therapeutic effects, encompassing anti-inflammatory, antioxidant, energy metabolism modulation, and antiplatelet aggregation properties. CONCLUSION THSWD exhibited protective effects on cerebral vascular structure and function and facilitated angiogenesis by rectifying cerebral microvascular metabolic disturbances in MCAO/R rats. Furthermore, integrated pharmacology offers a promising approach for studying the intricate traditional Chinese medicine (TCM) system in IS treatment.
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Affiliation(s)
- Linfeng Tang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Dandan Wang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Hao Chang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Zhuqing Liu
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Xueting Zhang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Xuefeng Feng
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230031, China
| | - Lan Han
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, 230012, China.
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Bai D, Wang Z, Xiao Y, Liu T, Pu Y, Sun H, Wang M, Guo C, Zhang J. Transdermal delivery of elastin peptide assisted by betaine-based deep eutectic solvent to ameliorate skin photoaging. BIOMATERIALS ADVANCES 2024; 163:213965. [PMID: 39053386 DOI: 10.1016/j.bioadv.2024.213965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/10/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The unique amino acid composition of elastin peptide (EP) makes it an excellent resource to obtain antioxidant peptides. It exhibits high elastase inhibitory activity with the potential to resist skin aging and is currently used in a many cosmetic products. However, the inherent low permeability of the skin limits its ability to penetrate the skin. To address this issue, a deep eutectic solvent (SAB) with excellent bioactivity was synthesized from betaine and succinic acid and used as a permeation enhancer to improve the absorption and utilization of EP in this paper. The results showed that low SAB concentrations significantly increased the transdermal delivery of EP. The 3D epidermal skin model (EpiKutis®) demonstrated that SAB/EP induced the synthesis of hyaluronic acid (HA) and filaggrin (FLG), accelerated skin barrier repair, and reduced water loss. Additionally, the zebrafish embryonic model showed that SAB/EP could reduce melanin secretion, decrease melanin deposition, and have an ameliorative effect on skin photoaging. Cellular experiments proved that SAB/EP can stimulate human skin fibroblasts to secrete procollagen I and elastin, improving skin elasticity and anti-wrinkle. The combination of EP and DES is a new attempt that is expected to be used as a safe and effective anti-wrinkle cosmetic material.
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Affiliation(s)
- De Bai
- Sauvage Laboratory for Smart Materials, Harbin Institute of Technology, Shenzhen 518055, PR China; State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, Shenzhen 518055, PR China; Research Centre of Printed Flexible Electronics, School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, PR China
| | - Zhenyuan Wang
- Shenzhen Shinehigh Innovation technology LTD., Shenzhen 518055, PR China
| | - Yuan Xiao
- Guangdong Marubi Biotechnol Co Ltd, Guangzhou 510700, PR China
| | - Tianqi Liu
- Sauvage Laboratory for Smart Materials, Harbin Institute of Technology, Shenzhen 518055, PR China; State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, Shenzhen 518055, PR China; Research Centre of Printed Flexible Electronics, School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, PR China
| | - Yan Pu
- Guangdong Marubi Biotechnol Co Ltd, Guangzhou 510700, PR China
| | - Huaiqing Sun
- Guangdong Marubi Biotechnol Co Ltd, Guangzhou 510700, PR China
| | - Mi Wang
- Sauvage Laboratory for Smart Materials, Harbin Institute of Technology, Shenzhen 518055, PR China; State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, Shenzhen 518055, PR China; Research Centre of Printed Flexible Electronics, School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, PR China.
| | - Chaowan Guo
- Guangdong Marubi Biotechnol Co Ltd, Guangzhou 510700, PR China.
| | - Jiaheng Zhang
- Sauvage Laboratory for Smart Materials, Harbin Institute of Technology, Shenzhen 518055, PR China; State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, Shenzhen 518055, PR China; Research Centre of Printed Flexible Electronics, School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, PR China; Shenzhen Shinehigh Innovation technology LTD., Shenzhen 518055, PR China.
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Zheng X, Hu Z, Gao S, Li Z, Chen J, Zhang G, Kong N, Sun J, Liu W. One-pot assay using a target-driven split aptamer recognition and assembly strategy for convenient and rapid detection of gliotoxin. Food Chem 2024; 454:139738. [PMID: 38820643 DOI: 10.1016/j.foodchem.2024.139738] [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: 12/23/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
An aptamer targeting gliotoxin (GTX) was optimized to increase the binding affinity by approximately 20 times and achieve higher structural stability and targeting specificity. Molecular dynamics simulations were used to explore the molecular mechanism and key action sites underlying the recognition of GTX by the optimized aptamer. Subsequently, the optimized aptamer was split into two fragments and a convenient and rapid one-pot assay for GTX detection was successfully established using a target-driven split aptamer recognition and assembly strategy. The method exhibited a good linear range of 0.128 nM to 2 μM, a low detection limit of 0.07 nM, and excellent selectivity for GTX. Furthermore, the method had good accuracy and stability in real sample analysis. Therefore, the developed one-pot method provides a reliable, convenient, and cost-effective approach for the widespread application of GTX detection.
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Affiliation(s)
- Xin Zheng
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Zunqi Hu
- Department of General Surgery, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Shunxiang Gao
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China.
| | - Zhen Li
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jia Chen
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Guanyi Zhang
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Nana Kong
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jianguo Sun
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China
| | - Weiwei Liu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
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10
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Li R, Zhu Q, Sun X, Li Z, Liu X. Electrochemical biosensor based on the integration of maple leaf-like gold nanocrystal and truncated aptamer for detection of α-amanitin with high sensitivity, selectivity and rapidity. Food Chem 2024; 453:139639. [PMID: 38759442 DOI: 10.1016/j.foodchem.2024.139639] [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: 02/09/2024] [Revised: 04/01/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
This study reports the fabrication of three-dimensional gold nanocrystals as sensing material in the presence of l-glutathion and high-performance aptamer with 20 bases of α-amanitin via truncation and optimization of along aptamer. The resulting maple leaf-like gold nanocrystal (ML-Au) exhibits an improved catalytic activity due to more exposed high-index facets. The use of truncated aptamer increases the sensitivity by 15 times and reduces the reaction time by two times compared with those of original aptamer. An α-amanitin electrochemical biosensor constructed by integrating ML-Au nanocrystals with truncated aptamer exhibits high sensitivity, selectivity and rapidity. An increase of the α-amanitin concentration in the range of 1 × 10-14-1 × 10-9 M causes a linear decrease in the amperometric current with a limit of detection of 2.9 × 10-15 M (S/N = 3). The proposed analytical method is satisfactorily used for electrochemical sensing of α-amanitin in urine and wild mushroom samples.
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Affiliation(s)
- Ruiyi Li
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, School of Life Sciences and Health Engineering, and School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qiyue Zhu
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, School of Life Sciences and Health Engineering, and School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiulan Sun
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, School of Life Sciences and Health Engineering, and School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zaijun Li
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, School of Life Sciences and Health Engineering, and School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Xiaohao Liu
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, School of Life Sciences and Health Engineering, and School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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Zeng Z, Hu Y, Xiang J, Su J, Tan H, Lai T, Chen X, Fang G, Li L, Luo L. Cucurbitacin B targets STAT3 to induce ferroptosis in non-small cell lung cancer. Eur J Pharmacol 2024; 978:176805. [PMID: 38950838 DOI: 10.1016/j.ejphar.2024.176805] [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: 03/12/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
Cucurbitacin B (CuB) is a compound found in plants like Cucurbitaceae that has shown promise in fighting cancer, particularly in lung cancer. However, the specific impact of CuB on ferroptosis and how it works in lung cancer cells has not been fully understood. Our research has discovered that CuB can effectively slow down the growth of non-small cell lung cancer (NSCLC) cells. Even in small amounts, it was able to inhibit the growth of various NSCLC cell lines. This inhibitory effect was reversed when ferroptosis inhibitors DFO, Lip-1 and Fer-1 were introduced. CuB was found to increase the levels of reactive oxygen species (ROS), lipid ROS, MDA, and ferrous ions within H358 lung cancer cells, leading to a decrease in GSH, mitochondrial membrane potential (MMP) and changes in ferroptosis-related proteins in a dose-dependent manner. These findings were also confirmed in A549 lung cancer cells. In A549 cells, different concentrations of CuB induced the accumulation of intracellular lipid ROS, ferrous ions and changes in ferroptosis-related indicators in a concentration-dependent manner. Meanwhile, the cytotoxic effect induced by CuB in A549 cells was counteracted by ferroptosis inhibitors DFO and Fer-1. Through network pharmacology, we identified potential targets related to ferroptosis in NSCLC cells treated with CuB, with STAT3 targets showing high scores. Further experiments using molecular docking and cell thermal shift assay (CETSA) revealed that CuB interacts with the STAT3 protein. Western blot and immunofluorescence staining demonstrated that CuB inhibits the phosphorylation of STAT3 (P-STAT3) in H358 cells. Silencing STAT3 enhanced CuB-induced accumulation of lipid ROS and iron ions, as well as the expression of ferroptosis-related proteins. On the other hand, overexpression of STAT3 reversed the effects of CuB-induced ferroptosis. The results indicate that CuB has the capability to suppress STAT3 activation, resulting in ferroptosis, and could be a promising treatment choice for NSCLC.
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Affiliation(s)
- Zeyao Zeng
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yingying Hu
- Department of Pathophysiology, Guangdong Medical University, Zhanjiang, 524002, Guangdong, China
| | - Jing Xiang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Jiating Su
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Huiting Tan
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Tianli Lai
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Xinming Chen
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Guixuan Fang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Li Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
| | - Lianxiang Luo
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
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12
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Guan L, Tan J, Qi B, Chen Y, Cao M, Zhang Q, Zou Y. Effects of an external static EF on the conformational transition of 5-HT1A receptor: A molecular dynamics simulation study. Biophys Chem 2024; 312:107283. [PMID: 38941873 DOI: 10.1016/j.bpc.2024.107283] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
The serotonin receptor subtype 1A (5-HT1AR), one of the G-protein-coupled receptor (GPCR) family, has been implicated in several neurological conditions. Understanding the activation and inactivation mechanism of 5-HT1AR at the molecular level is critical for discovering novel therapeutics in many diseases. Recently there has been a growing appreciation for the role of external electric fields (EFs) in influencing the structure and activity of biomolecules. In this study, we used molecular dynamics (MD) simulations to examine conformational features of active states of 5-HT1AR and investigate the effect of an external static EF with 0.02 V/nm applied on the active state of 5-HT1AR. Our results showed that the active state of 5-HT1AR maintained the native structure, while the EF led to structural modifications in 5-HT1AR, particularly inducing the inward movement of transmembrane helix 6 (TM6). Furthermore, it disturbed the conformational switches associated with activation in the CWxP, DRY, PIF, and NPxxY motifs, consequently predisposing an inclination towards the inactive-like conformation. We also found that the EF led to an overall increase in the dipole moment of 5-HT1AR, encompassing TM6 and pivotal amino acids. The analyses of conformational properties of TM6 showed that the changed secondary structure and decreased solvent exposure occurred upon the EF condition. The interaction of 5-HT1AR with the membrane lipid bilayer was also altered under the EF. Our findings reveal the molecular mechanism underlying the transition of 5-HT1AR conformation induced by external EFs, which offer potential novel insights into the prospect of employing structure-based EF applications for GPCRs.
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Affiliation(s)
- Lulu Guan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Jingwang Tan
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Bote Qi
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Yukang Chen
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China
| | - Meng Cao
- Department of Physical Education, College of Sport, Shenzhen University, 3688 Nanhai Road, Shenzhen, Guangdong 518061, PR China
| | - Qingwen Zhang
- College of Physical Education, Shanghai University of Sport, 399 Changhai Road, Shanghai 200438, PR China
| | - Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, PR China.
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13
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Gavalda-Garcia J, Bickel D, Roca-Martinez J, Raimondi D, Orlando G, Vranken W. Data-driven probabilistic definition of the low energy conformational states of protein residues. NAR Genom Bioinform 2024; 6:lqae082. [PMID: 38984065 PMCID: PMC11231583 DOI: 10.1093/nargab/lqae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/14/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
Protein dynamics and related conformational changes are essential for their function but difficult to characterise and interpret. Amino acids in a protein behave according to their local energy landscape, which is determined by their local structural context and environmental conditions. The lowest energy state for a given residue can correspond to sharply defined conformations, e.g. in a stable helix, or can cover a wide range of conformations, e.g. in intrinsically disordered regions. A good definition of such low energy states is therefore important to describe the behaviour of a residue and how it changes with its environment. We propose a data-driven probabilistic definition of six low energy conformational states typically accessible for amino acid residues in proteins. This definition is based on solution NMR information of 1322 proteins through a combined analysis of structure ensembles with interpreted chemical shifts. We further introduce a conformational state variability parameter that captures, based on an ensemble of protein structures from molecular dynamics or other methods, how often a residue moves between these conformational states. The approach enables a different perspective on the local conformational behaviour of proteins that is complementary to their static interpretation from single structure models.
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Affiliation(s)
- Jose Gavalda-Garcia
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - David Bickel
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joel Roca-Martinez
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | | | | | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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14
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Moffa S, Carradori S, Melfi F, Fontana A, Ciulla M, Di Profio P, Aschi M, Wolicki RD, Pilato S, Siani G. Fine-tuning of membrane permeability by reversible photoisomerization of aryl-azo derivatives of thymol embedded in lipid nanoparticles. Colloids Surf B Biointerfaces 2024; 241:114043. [PMID: 38901266 DOI: 10.1016/j.colsurfb.2024.114043] [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: 03/14/2024] [Revised: 06/07/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
Responsiveness of liposomes to external stimuli, such as light, should allow a precise spatial and temporal control of release of therapeutic agents or ion transmembrane transport. Here, some aryl-azo derivatives of thymol are synthesized and embedded into liposomes from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine to obtain light-sensitive membranes whose photo-responsiveness, release behaviour, and permeability towards Cl- ions are investigated. The hybrid systems are in-depth characterized by dynamic light scattering, atomic force microscopy and Raman spectroscopy. In liposomal bilayer the selected guests undergo reversible photoinduced isomerization upon irradiation with UV and visible light, alternately. Non-irradiated hybrid liposomes retain entrapped 5(6)-carboxyfluorescein (CF), slowing its spontaneous leakage, whereas UV-irradiation promotes CF release, due to guest trans-to-cis isomerization. Photoisomerization also influences membrane permeability towards Cl- ions. Data processing, according to first-order kinetics, demonstrates that Cl- transmembrane transport is enhanced by switching the guest from trans to cis but restored by back-switching the guest from cis to trans upon illumination with blue light. Finally, the passage of Cl- ions across the bilayer can be fine-tuned by irradiation with light of longer λ and different light-exposure times. Fine-tuning the photo-induced structural response of the liposomal membrane upon isomerization is a promising step towards effective photo-dynamic therapy.
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Affiliation(s)
- Samanta Moffa
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy
| | - Simone Carradori
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy
| | - Francesco Melfi
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy
| | - Antonella Fontana
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy; UdA-TechLab, Research Center, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy
| | - Michele Ciulla
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy; UdA-TechLab, Research Center, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy
| | - Pietro Di Profio
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell'Aquila, via Vetoio, Coppito, L'Aquila 67100, Italy
| | - Rafal Damian Wolicki
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy
| | - Serena Pilato
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy; UdA-TechLab, Research Center, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy.
| | - Gabriella Siani
- Dipartimento di Farmacia, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy; UdA-TechLab, Research Center, Università degli Studi Gabriele d'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti 66100, Italy.
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15
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Şenel P, Faysal AA, Erdoğan T, Doğan M, Gölcü A. Quantitative study on a simple electrochemical dsDNA-pregabalin biosensor; multi-spectroscopic, molecular docking and modelling studies. J Pharm Biomed Anal 2024; 247:116261. [PMID: 38823224 DOI: 10.1016/j.jpba.2024.116261] [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: 02/23/2024] [Revised: 05/13/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Pregabalin (PGB) is a γ-aminobutyric acid (GABA) alkylated analog prescribed to treat neuropathic pain, fibromyalgia, and postherpetic neuralgia. Using analytical, spectroscopic methods and molecular docking and molecular dynamics (MD) simulations, a detailed experimental and theoretical investigation was conducted into the binding process and interactions between PGB and double-stranded fish sperm deoxyribonucleic acid (dsDNA). It was evident from the collected experimental results that PGB binds with ds-DNA. PGB attaches to dsDNA via minor groove binding, as demonstrated by the results of electrochemical studies, UV-Vis absorption spectroscopy, and replacement study with ethidium bromide and Hoechst-32588. PGB's binding constant (Kb) with dsDNA, as determined by the Benesi-Hildebrand plot, is 2.41×104 ± 0.30 at 298 K. The fluorescence investigation indicates that PGB and dsDNA have a binding stoichiometry (n) of 1.21 ± 0.09. Molecular docking simulations were used in the research to computational determination of the interactions between PGB and dsDNA. The findings demonstrated that minor groove binding was the mechanism by which PGB interacted with dsDNA. Based on the electrochemically responsive PGB-dsDNA biosensor, we developed a technique for low-concentration detection of PGB utilizing differential pulse voltammetry (DPV). The voltammetric analysis of the peak current decrease in the deoxyadenosine oxidation signals resulting from the association between PGB and dsDNA enabled a sensitive estimation of PGB in pH 4.80 acetate buffer. The deoxyguanosine oxidation signals exhibited a linear relationship between 2 and 16 μM PGB. The values for the limit of detection (LOD) and limit of quantitation (LOQ) were 0.57 μM and 1.91 μM, respectively.
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Affiliation(s)
- Pelin Şenel
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Istanbul, Turkiye
| | - Abdullah Al Faysal
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Istanbul, Turkiye
| | - Taner Erdoğan
- Kocaeli University, Kocaeli Vocational School, Department of Chemistry and Chemical Processing Technologies, Kocaeli, Turkiye
| | - Mustafa Doğan
- Istanbul Technical University, Faculty of Electrical-Electronics Engineering, Department of Control and Automation Engineering, Istanbul, Turkiye
| | - Ayşegül Gölcü
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Istanbul, Turkiye.
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16
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Yang B, Zhao T, Ji S, Liu Y, Xu M, Lu B. Molecular dynamics simulations of the interfacial behaviors and photo-oxidation of phytosterol under different emulsion oil content. Food Chem 2024; 451:139292. [PMID: 38663239 DOI: 10.1016/j.foodchem.2024.139292] [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: 12/01/2023] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 05/26/2024]
Abstract
Phytosterol, recognized for its health benefits, is predominantly extracted from plants and exhibits significantly reduced stability under varying light conditions. Their photooxidation is significantly influenced by emulsion interfaces. This study examined the mechanism of interface structure on phytosterol photooxidation with unparalleled molecular precision, utilizing molecular dynamics simulations and experimental procedures. Hydrogen bonding between the hydroxyl group at the C3 position of phytosterols and water molecules, coupled with van der Waals forces between the hydrophobic regions and the oil phase, induced phytosterol molecules to disperse toward the interface. The elevated polarity of the oil phase, specifically in tributyrin, facilitated the permeation of water molecules into the oil phase. This was achieved by diminishing the emulsion's interfacial tension, thereby fostering the development of more interface or micelles, and accelerating the photooxidation process of phytosterols. These simulations unraveled that the preponderance of phytosterol distribution is localized and oxidized at the oil-water interface.
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Affiliation(s)
- Bowen Yang
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Tian Zhao
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Shengyang Ji
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yan Liu
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Minghao Xu
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Baiyi Lu
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Key Laboratory for Agro-Products Nutritional Evaluation of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agro-Food Processing, Ningbo Research Institute, Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
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17
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Aram C, Alijanizadeh P, Saleki K, Karami L. Development of an ancestral DC and TLR4-inducing multi-epitope peptide vaccine against the spike protein of SARS-CoV and SARS-CoV-2 using the advanced immunoinformatics approaches. Biochem Biophys Rep 2024; 39:101745. [PMID: 38974021 PMCID: PMC11225186 DOI: 10.1016/j.bbrep.2024.101745] [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: 03/12/2024] [Revised: 04/26/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024] Open
Abstract
The oldest human coronavirus that started pandemics is severe acute respiratory syndrome virus (SARS-CoV). While SARS-CoV was eradicated, its new version, SARS-CoV2, caused the global pandemic of COVID-19. Evidence highlights the harmful events orchestrated by these viruses are mediated by Spike (S)P protein. Experimental epitopes of the S protein which were overlapping and ancestral between SARS-CoV and SARS-CoV-2 were obtained from the immune epitopes database (IEDB). The epitopes were then assembled in combination with a 50 S ribosomal protein L7/L12 adjuvant, a Mycobacterium tuberculosis-derived element and mediator of dendritic cells (DCs) and toll-like receptor 4 (TLR4). The immunogenic sequence was modeled by the GalaxyWeb server. After the improvement and validation of the protein structure, the physico-chemical properties and immune simulation were performed. To investigate the interaction with TLR3/4, Molecular Dynamics Simulation (MDS) was used. By merging the 17 B- and T-lymphocyte (HTL/CTL) epitopes, the vaccine sequence was created. Also, the Ramachandran plot presented that most of the residues were located in the most favorable and allowed areas. Moreover, SnapGene was successful in cloning the DNA sequence linked to our vaccine in the intended plasmid. A sequence was inserted between the XhoI and SacI position of the pET-28a (+) vector, and simulating the agarose gel revealed the existence of the inserted gene in the cloned plasmid with SARS vaccine (SARSV) construct, which has a 6565 bp in length overall. In terms of cytokines/IgG response, immunological simulation revealed a strong immune response. The stabilized vaccine showed strong interactions with TLR3/4, according to Molecular Dynamics Simulation (MDS) analysis. The present ancestral vaccine targets common sequences which seem to be valuable targets even for the new variant SARS-CoV-2.
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Affiliation(s)
- Cena Aram
- Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Parsa Alijanizadeh
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Kiarash Saleki
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Leila Karami
- Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
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18
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Ahmed AA, Morshedizad M, Kühn O, Leinweber P. Deciphering competitive interactions: Phosphate and organic matter binding on goethite through experimental and theoretical insights. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173510. [PMID: 38806124 DOI: 10.1016/j.scitotenv.2024.173510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
The adsorption of phosphorus (P) onto active soil surfaces plays a pivotal role in immobilizing P, thereby influencing soil fertility and the filter function of soil to protect freshwater systems from eutrophication. Competitive anions, such as organic matter (OM), significantly affect the strength of this P-binding, eventually controlling P mobility and release, but surprisingly, these processes are insufficiently understood at the molecular level. In this study, we provide a molecular-level perspective on the influence of OM on P binding at the goethite-water interface using a combined experimental-theoretical approach. By examining the impact of citric acid (CIT) and histidine (HIS) on the adsorption of orthophosphate (OP), glycerol phosphate (GP), and inositol hexaphosphate (IHP) through adsorption experiments and molecular dynamics simulations, we address fundamental questions regarding P binding trends, OM interaction with the goethite surface, and the effect of OM on P adsorption. Our findings reveal the complex nature of P adsorption on goethite surfaces, where the specific OM, treatment conditions (covering the surface with OM or simultaneous co-adsorption), and initial concentrations collectively shape these interactions. P adsorption on goethite exhibits a binding strength increasing in the order of GP < OP < IHP. Crucially, this trend remains consistent across all adsorption experiments, regardless of the presence or absence of OM, CIT, or HIS, and irrespective of the specific treatment method. Notably, OP is particularly susceptible to inhibition by OM, while adsorption of GP depends on specific OM treatments. Despite being less sensitive to OM, IHP shows reduced adsorption, especially at higher initial P concentrations. Of significance is the strong inhibitory effect of CIT, particularly evident when the surface is pre-covered, resulting in a substantial 70 % reduction in OP adsorption compared to bare goethite. The sequence of goethite binding affinity to P and OM underscores a higher affinity of CIT and HIS compared to OP and GP, suggesting that OM can effectively compete with both OP and GP and replace them at the surface. In contrast, the impact of OM on IHP adsorption appears insignificant, as IHP exhibits a higher affinity than both CIT and HIS towards the goethite surface. The coverage of goethite surfaces with OM results in the blocking of active sites and the generation of an unfavorable electric potential and field, inhibiting anion adsorption and consequently reducing P binding. It is noteworthy that electrostatic interactions predominantly contribute more to the binding of P and OM to the surface compared to dispersion interactions.
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Affiliation(s)
- Ashour A Ahmed
- Institute of Physics, University of Rostock, Albert-Einstein-Str. 23-24, D-18059 Rostock, Germany.
| | - Mohsen Morshedizad
- Chair of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, D-18059 Rostock, Germany
| | - Oliver Kühn
- Institute of Physics, University of Rostock, Albert-Einstein-Str. 23-24, D-18059 Rostock, Germany
| | - Peter Leinweber
- Chair of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, D-18059 Rostock, Germany
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19
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Wang M, Aalling-Frederiksen O, Madsen AØ, Jensen KMØ, Jørgensen MRV, Gong J, Rades T, Martins ICB. Different or the same? exploring the physicochemical properties and molecular mobility of celecoxib amorphous forms. Int J Pharm 2024; 661:124470. [PMID: 39004294 DOI: 10.1016/j.ijpharm.2024.124470] [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: 05/24/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
The influence of different preparation methods on the physicochemical properties of amorphous solid forms have gained considerable attention, especially with recent publications on pharmaceutical polyamorphism. In the present study, we have investigated the possible occurrence of polyamorphism in the drug celecoxib (CEL) by investigating the thermal behavior, morphology, structure, molecular mobility and physical stability of amorphous CEL obtained by quench-cooling (QC), ball milling (BM) and spray drying (SD). Similar glass transition temperatures but different recrystallization behaviors were observed for CEL-QC, CEL-BM and CEL-SD using modulated differential scanning calorimetry analysis. A correlation between the different recrystallization behaviors of the three CEL amorphous forms and the respective distinct powder morphologies, was also found. Molecular dynamics simulations however, reveal that CEL presents similar molecular conformational distributions when subjected to QC and SD. Moreover, the obtained molecular conformational distributions of CEL are different from the ones found in its crystal structure and also from the ones found in the lowest-energy structure obtained by quantum mechanical calculations. The type and strength of CEL hydrogen bond interactions found in CEL-QC and CEL-SD systems are almost identical, though different from the ones presented in the crystal structure. Pair distribution function analyses and isothermal microcalorimetry show similar local structures and structural relaxation times, respectively, for CEL-QC, CEL-BM and CEL-SD. The present work shows that not only similar physicochemical properties (glass transition temperature, and structural relaxation time), but also similar molecular conformational distributions were observed for all prepared CEL amorphous systems. Hence, despite their different recrystallization behaviors, the three amorphous forms of CEL did not show any signs of polyamorphism.
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Affiliation(s)
- Mengwei Wang
- School of Pharmacy, Henan University, Kaifeng, China; Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, China
| | | | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kirsten M Ø Jensen
- Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Mads R V Jørgensen
- Department of Chemistry & iNANO, Aarhus University, Aarhus, Denmark; MAX IV Laboratory, Lund University, Lund, Sweden
| | - Junbo Gong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, China
| | - Thomas Rades
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
| | - Inês C B Martins
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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20
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Feizpour R, Jabbari A, Hadizadeh F, Alibolandi M, Ramezani M, Saberi MR, Taghdisi SM, Abnous K. Targeted delivery of SN38 to breast cancer using amphiphilic diblock copolymers PHPMA-b-PBAEM as micellar carriers with AS1411 aptamer. Int J Pharm 2024; 661:124387. [PMID: 38925238 DOI: 10.1016/j.ijpharm.2024.124387] [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: 04/15/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Breast cancer treatment can be challenging, but a targeted drug delivery system (DDS) has the potential to make it more effective and reduce side effects. This study presents a novel nanotherapeutic targeted DDS developed through the self-assembly of an amphiphilic di-block copolymer to deliver the chemotherapy drug SN38 specifically to breast cancer cells. The vehicle was constructed from the PHPMA-b-PEAMA diblock copolymer synthesized via RAFT polymerization. A single emulsion method was then used to encapsulate SN38 within nanoparticles (NPs) formed from the PHPMA-b-PEAMA copolymer. The AS1411 DNA aptamer was covalently bonded to the surface of the micellar NPs, producing a targeted DDS. Molecular dynamics (MD) simulation studies were also performed on the di block polymeric system, demonstrating that SN38 interacted well with the di block. The in vitro results demonstrated that AS1411- decorated SN38-loaded HPMA NPs were highly toxic to breast cancer cells while having a minimal effect on non-cancerous cells. Remarkably, in vivo studies elucidated the ability of the targeted DDS to enhance the antitumor effect of SN38, suppressing tumor growth and improving survival rates compared to free SN38.
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Affiliation(s)
- Rozita Feizpour
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atena Jabbari
- UCLA, Department of Chemistry and Biochemistry, Los Angeles CA 90095, USA
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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21
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Devereux M, Boittier ED, Meuwly M. Systematic improvement of empirical energy functions in the era of machine learning. J Comput Chem 2024; 45:1899-1913. [PMID: 38695412 DOI: 10.1002/jcc.27367] [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: 10/31/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 07/05/2024]
Abstract
The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (CH 2 Cl 2 ), and solvated K + and Cl - ions. For the electrostatic interactions, point charges (PCs) and machine learning (ML)-based minimally distributed charges (MDCM) fitted to the molecular electrostatic potential are evaluated together with electrostatics based on the Coulomb integral. The impact of explicitly including second-order terms is investigated by adding a fragment molecular orbital (FMO)-derived polarization energy to an existing force field, in this case CHARMM. It is demonstrated that anisotropic electrostatics reduce the RMSE for water (by 1.4 kcal/mol), CH 2 Cl 2 (by 0.8 kcal/mol) and for solvated Cl - clusters (by 0.4 kcal/mol). An additional polarization term can be neglected for CH 2 Cl 2 but further improves the models for pure water (by ∼ 1.0 kcal/mol) and hydrated Cl - (by 0.4 kcal/mol), and is key for solvated K + , reducing the RMSE by 2.3 kcal/mol. A 12-6 Lennard-Jones functional form performs satisfactorily with PC and MDCM electrostatics, but is not appropriate for descriptions that account for the electrostatic penetration energy. The importance of many-body contributions is assessed by comparing a strictly 2-body approach with self-consistent reference data. Two-body interactions suffice for CH 2 Cl 2 whereas water and solvated K + and Cl - ions require explicit many-body corrections. Finally, a many-body-corrected dimer potential energy surface exceeds the accuracy attained using a conventional empirical force field, potentially reaching that of an FMO calculation. The present work systematically quantifies which terms improve the performance of an existing force field and what reference data to use for parametrizing these terms in a tractable fashion for ML fitting of pure and heterogeneous systems.
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Affiliation(s)
- Mike Devereux
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
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22
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Torrejón MJ, Algaba J, Blas FJ. Dissociation line and driving force for nucleation of the nitrogen hydrate from computer simulation. II. Effect of multiple occupancy. J Chem Phys 2024; 161:054712. [PMID: 39092957 DOI: 10.1063/5.0220098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500 bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500 bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation.
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Affiliation(s)
- Miguel J Torrejón
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - Jesús Algaba
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
| | - Felipe J Blas
- Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, 21006 Huelva, Spain
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23
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Zhang N, Zhu Y, Li YN, Zhang LR, Zhang FS, Liu JJ. Design of eco-friendly antifreeze peptides as novel inhibitors of gas-hydration kinetics. J Chem Phys 2024; 161:054701. [PMID: 39087548 DOI: 10.1063/5.0211732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
In this study, peptides designed using fragments of an antifreeze protein (AFP) from the freeze-tolerant insect Tenebrio molitor, TmAFP, were evaluated as inhibitors of clathrate hydrate formation. It was found that these peptides exhibit inhibitory effects by both direct and indirect mechanisms. The direct mechanism involves the displacement of methane molecules by hydrophobic methyl groups from threonine residues, preventing their diffusion to the hydrate surface. The indirect mechanism is characterized by the formation of cylindrical gas bubbles, the morphology of which reduces the pressure difference at the bubble interface, thereby slowing methane transport. The transfer of methane to the hydrate interface is primarily dominated by gas bubbles in the presence of antifreeze peptides. Spherical bubbles facilitate methane migration and potentially accelerate hydrate formation; conversely, the promotion of a cylindrical bubble morphology by two of the designed systems was found to mitigate this effect, leading to slower methane transport and reduced hydrate growth. These findings provide valuable guidance for the design of effective peptide-based inhibitors of natural-gas hydrate formation with potential applications in the energy and environmental sectors.
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Affiliation(s)
- Nan Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Ying Zhu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yan-Nan Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Li-Rong Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Feng-Shou Zhang
- The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China
| | - Jun-Jie Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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24
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Yang P, Kumarasiri A, Hore D. Surface populations as a model for the distance-dependence of the interfacial refractive index. J Chem Phys 2024; 161:054703. [PMID: 39087546 DOI: 10.1063/5.0221234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Vibrational sum frequency spectra provide information about interfaces that is sensitive to the orientation of molecules, their electronic environment, and the local electric fields. Here, we use molecular dynamics simulations in order to study a surfactant, para-cyanophenol, at the air-water interface. The volume fractions of water and the organic surfactant are considered at various points over the nanometer-scale region in a Lorentz-Lorenz model. We find that the calculated ratios of nonlinear susceptibility tensor elements are in agreement with experimental data only when this depth profile was considered. We also use these data to evaluate the ratio of the C-N hyperpolarizability tensor elements in the interfacial region.
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Affiliation(s)
- Peter Yang
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Aruna Kumarasiri
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Dennis Hore
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
- Department of Computer Science, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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25
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Ono Y, Yamamoto E, Yasuoka K. Water structures in tip-charged carbon nanotubes. J Chem Phys 2024; 161:054702. [PMID: 39087547 DOI: 10.1063/5.0218315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/14/2024] [Indexed: 08/02/2024] Open
Abstract
Carbon nanotubes (CNTs) have potential applications in separation membranes and nanofluidic devices. It is well known that the behavior of water molecules confined in CNTs is affected by surface functional groups and external electric fields, leading to structural changes. The understanding of these structural changes of water within various CNTs is crucial, particularly in the context of material separation. While there have been many investigations into the effects of individual specific functional groups, a comprehensive understanding of the effect of these functional groups and the electric fields they generate on water molecules remains elusive. In this study, we investigate the properties of water molecules in tip-charged CNTs of (8,8), (10,10), and (12,12) chiral vectors with positive charges at one tip and negative charges at the other tip. Abstraction of ionized functional groups as tip charges enables a comprehensive understanding that is independent of individual functional groups. The symmetrically arranged tip-charges spontaneously generate a strong and symmetric electric field in the CNTs. However, the strength and directionality of the electric field are non-uniform and complex. In the interiors of (8,8) and (10,10) tip-charged CNTs, helical and square structures, which have disturbances caused by the non-uniformity of the electric field, are observed. The properties of the water molecules differed significantly in the center of the CNTs and near positive and negative charges, despite the electric field symmetry. In (12,12) tip-charged CNTs with 12 charges, a local ring structure is observed in the vicinity of negative charges but not in the vicinity of positive charges. It is concluded that the water structures in tip-charged CNTs have different characteristics from those in plain CNTs under a uniform electric field.
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Affiliation(s)
- Yûi Ono
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Eiji Yamamoto
- Department of System Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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26
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Shen L, Sun F, Wang Y, Liu Y, Xin Q, Zhu Z, Zhang H, Xu X, Ding C, Zheng L, Li J. Caries-Prone Primary Teeth: A Hidden Reason and Prophylactic Treatment in the Viewpoint of Materials Science. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39092619 DOI: 10.1021/acsami.4c07388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Dental caries, the most prevalent chronic disease across all age groups, has a high prevalence, particularly among children. However, there is no specific and effective treatment for the prevention of caries in primary teeth (Pr.T.), which stems from a lack of knowledge regarding the basic nature of the tooth surface. Herein, we observed that the adhesion energies of the caries-related bacteria Streptococcus mutans and Streptococcus sanguinis to Pr.T were approximately 10 and 5.5 times higher than those to permanent teeth (Pe.T). A lower degree of mineralization and more hydrophilic characteristics of the Pr.T enamel account for this discrepancy. Accordingly, we proposed that the on-target modification of both hydroxyapatite and organic components on Pr.T by dual modification would render a sufficient hydration layer. This resulted in an approximately 11-time decrease in bacterial adhesion energy after treatment. In contrast, a single hydroxyapatite modification on Pe.T and young permanent teeth (Y.Pe.T) was sufficient to achieve a similar effect. Theoretical simulation further verified the rationality of the approach. Our findings may help understand the reason for Pr.T being caries-prone and provide references for treatment using resin restorations. This strategy offers valuable insights into daily oral hygiene and dental prophylactic treatment in children.
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Affiliation(s)
- Luxuan Shen
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Fan Sun
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Yu Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Qiangwei Xin
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Zhongpeng Zhu
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu 215123, China
| | - Hongbo Zhang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Xinyuan Xu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Chunmei Ding
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jianshu Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Med-X Center for Materials, Sichuan University, Chengdu 610017, China
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27
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Krishna NB, Roopa L, Pravin Kumar R, S GT. Computational studies on the catalytic potential of the double active site for enzyme engineering. Sci Rep 2024; 14:17892. [PMID: 39095391 DOI: 10.1038/s41598-024-60824-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/27/2024] [Indexed: 08/04/2024] Open
Abstract
Proteins possessing double active sites have the potential to revolutionise enzyme design strategies. This study extensively explored an enzyme that contains both a natural active site (NAS) and an engineered active site (EAS), focusing on understanding its structural and functional properties. Metadynamics simulations were employed to investigate how substrates interacted with their respective active sites. The results revealed that both the NAS and EAS exhibited similar minimum energy states, indicating comparable binding affinities. However, it became apparent that the EAS had a weaker binding site for the substrate due to its smaller pocket and constrained conformation. Interestingly, the EAS also displayed dynamic behaviour, with the substrate observed to move outside the pocket, suggesting the possibility of substrate translocation. To gain further insights, steered molecular dynamics (SMD) simulations were conducted to study the conformational changes of the substrate and its interactions with catalytic residues. Notably, the substrate adopted distinct conformations, including near-attack conformations, in both the EAS and NAS. Nevertheless, the NAS demonstrated superior binding minima for the substrate compared to the EAS, reinforcing the observation that the engineered active site was less favourable for substrate binding due to its limitations. The QM/MM (Quantum mechanics and molecular mechanics) analyses highlight the energy disparity between NAS and EAS. Specifically, EAS exhibited elevated energy levels due to its engineered active site being located on the surface. This positioning exposes the substrate to solvents and water molecules, adding to the energy challenge. Consequently, the engineered enzyme did not provide a significant advantage in substrate binding over the single active site protein. Further, the investigation of internal channels and tunnels within the protein shed light on the pathways facilitating transport between the two active sites. By unravelling the complex dynamics and functional characteristics of this double-active site protein, this study offers valuable insights into novel strategies of enzyme engineering. These findings establish a solid foundation for future research endeavours aimed at harnessing the potential of double-active site proteins in diverse biotechnological applications.
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Affiliation(s)
- Naveen Banchallihundi Krishna
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
| | - Lalitha Roopa
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India
| | - R Pravin Kumar
- Department of Computational Biology and AI, Kcat Enzymatic Private Limited, #16, Ramakrishnappa Road, Cox Town, Bangalore, 560005, India.
| | - Gopenath T S
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, 570015, India
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28
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Piccoli V, Martínez L. Competitive Effects of Anions on Protein Solvation by Aqueous Ionic Liquids. J Phys Chem B 2024. [PMID: 39092664 DOI: 10.1021/acs.jpcb.4c03735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The present study utilizes molecular dynamics simulations to examine how different anions compete for protein solvation in aqueous solutions of ionic liquids (ILs). Ubiquitin is used as model protein and studied in IL mixtures sharing the same cation, 1-ethyl-3-methylimidazolium (EMIM), and two different anions in the same solution, from combinations of dicyanamide (DCA), chloride (Cl), nitrate (NO3), and tetrafluoroborate (BF4). Our findings reveal that specific interactions between anions and the protein are paramount in IL solvation, but that combinations of anions are not additive. For example, DCA exhibits a remarkable ability to form hydrogen bonds with the protein, resulting in a significantly stronger preferential binding to the protein than other anions. However, the combination of DCA with NO3, which also forms hydrogen bonds with the protein, results in a smaller preferential solvation of the protein than the combination of DCA with chloride ions, which are weaker binders. Thus, combining anions with varying affinities for the protein surface modulates the overall ion accumulation through nonadditive mechanisms, highlighting the importance of the understanding of competition for specific interaction sites, cooperative binding, bulk-solution affinity, and overall charge compensations, on the overall solvation capacity of the solution. Such knowledge may allow for the design of novel IL-based processes in biotechnology and material science, where fine-tuning protein solvation is crucial for optimizing performance and functionality.
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Affiliation(s)
- Vinicius Piccoli
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-872, SP, Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-872, SP, Brazil
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29
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Sarkar T, Vignesh SR, Sehgal T, Ronima KR, Thummer RP, Satpati P, Chatterjee S. Development of protease resistant and non-cytotoxic Jelleine analogs with enhanced broad spectrum antimicrobial efficacy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184336. [PMID: 38763273 DOI: 10.1016/j.bbamem.2024.184336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Short systemic half- life of Antimicrobial Peptides (AMP) is one of the major bottlenecks that limits their successful commercialization as therapeutics. In this work, we have designed analogs of the natural AMP Jelleine, obtained from royal jelly of apis mellifera. Among the designed peptides, J3 and J4 were the most potent with broad spectrum activities against a varied class of ESKAPE pathogens and fungus C. albicans. All the developed peptides were more effective against Gram-negative bacteria in comparison to the Gram-positive pathogens, and were especially effective against P. aeruginosa and C. albicans.J3 and J4 were completely trypsin resistant and serum stable, while retaining the non-cytotoxicity of the parent Jelleine, Jc. The designed peptides were membranolytic in their mode of action. CD and MD simulations in the presence of bilayers, established that J3 and J4 were non-structured even upon membrane binding and suggested that biological properties of the AMPs were innocent of any specific secondary structural requirements. Enhancement of charge to increase the antimicrobial potency, controlling the hydrophobic-hydrophilic balance to maintain non-cytotoxicity and induction of unnatural amino acid residues to impart protease resistance, remains some of the fundamental principles in the design of more effective antimicrobial therapeutics of the future, which may help combat the quickly rising menace of antimicrobial resistance in the microbes.
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Affiliation(s)
- Tanumoy Sarkar
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India
| | - S R Vignesh
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Tanya Sehgal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India
| | - K R Ronima
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Rajkumar P Thummer
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Priyadarshi Satpati
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India.
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India.
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30
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024; 92:905-922. [PMID: 38506327 PMCID: PMC11222054 DOI: 10.1002/prot.26685] [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: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824
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31
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Yu D, Li H, Liu Y, Yang X, Yang W, Fu Y, Zuo YA, Huang X. Application of the molecular dynamics simulation GROMACS in food science. Food Res Int 2024; 190:114653. [PMID: 38945587 DOI: 10.1016/j.foodres.2024.114653] [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: 02/01/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.
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Affiliation(s)
- Dongping Yu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Haiping Li
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China.
| | - Yuzi Liu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xingqun Yang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Wei Yang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yiran Fu
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yi-Ao Zuo
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xianya Huang
- Tianjin Key Laboratory of Food Biotechnology, Faculty of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
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Wasim A, Menon S, Mondal J. Modulation of α-synuclein aggregation amid diverse environmental perturbation. eLife 2024; 13:RP95180. [PMID: 39087984 PMCID: PMC11293868 DOI: 10.7554/elife.95180] [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] [Indexed: 08/02/2024] Open
Abstract
Intrinsically disordered protein α-synuclein (αS) is implicated in Parkinson's disease due to its aberrant aggregation propensity. In a bid to identify the traits of its aggregation, here we computationally simulate the multi-chain association process of αS in aqueous as well as under diverse environmental perturbations. In particular, the aggregation of αS in aqueous and varied environmental condition led to marked concentration differences within protein aggregates, resembling liquid-liquid phase separation (LLPS). Both saline and crowded settings enhanced the LLPS propensity. However, the surface tension of αS droplet responds differently to crowders (entropy-driven) and salt (enthalpy-driven). Conformational analysis reveals that the IDP chains would adopt extended conformations within aggregates and would maintain mutually perpendicular orientations to minimize inter-chain electrostatic repulsions. The droplet stability is found to stem from a diminished intra-chain interactions in the C-terminal regions of αS, fostering inter-chain residue-residue interactions. Intriguingly, a graph theory analysis identifies small-world-like networks within droplets across environmental conditions, suggesting the prevalence of a consensus interaction patterns among the chains. Together these findings suggest a delicate balance between molecular grammar and environment-dependent nuanced aggregation behavior of αS.
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Affiliation(s)
- Abdul Wasim
- Tata Institute of Fundamental ResearchHyderabadIndia
| | - Sneha Menon
- Tata Institute of Fundamental ResearchHyderabadIndia
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Endrakanti M, Sharma J, Ethayathulla AS, Kaur P, Khan SA, Kabra M, Gupta N. ECEL1 related distal arthrogryposis 5D in an Indian cohort-Report of recognizable musculoskeletal phenotype and a possible founder variant. Am J Med Genet A 2024; 194:e63592. [PMID: 38568023 DOI: 10.1002/ajmg.a.63592] [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: 07/30/2023] [Revised: 01/24/2024] [Accepted: 03/02/2024] [Indexed: 07/05/2024]
Abstract
Distal arthrogryposis type 5D (DA5D) is clinically characterized by knee extension contractures, distal joint contractures, clubfoot, micrognathia, ptosis, and scoliosis. We report nine affected individuals from eight unrelated Indian families with DA5D. Although the overall musculoskeletal phenotype is not very distinct from other distal arthrogryposis, the presence of fixed knee extension contractures with or without scoliosis could be an important early pointer to DA5D. We also report a possible founder variant in ECEL1 along with four novel variants and further expand the genotypic spectrum of DA5D.
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Affiliation(s)
- Mounika Endrakanti
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Sharma
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Shah Alam Khan
- Department of Orthopedics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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Yang P, Wu Q, Liu H, Zhou S, Chen W, Zhong H, Zhang K, Zou F, Ying H. Simulation and mechanism for the Ultrasound-Assisted Oiling-Out Process: A case study using Fructose-1,6-diphosphate. ULTRASONICS SONOCHEMISTRY 2024; 108:106953. [PMID: 38879963 PMCID: PMC11228588 DOI: 10.1016/j.ultsonch.2024.106953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/18/2024]
Abstract
Liquid-liquid separation, commonly referred to as oiling-out, frequently can occurs during crystallization, especially the anti-solvent crystallization process of phosphoryl compounds, and poses potential hurdle for high-quality product. Efficiently regulating oiling-out during crystallization remains a significant challenge. Among various techniques, ultrasound emerges as a green and effective approach to enhance the crystallization process. However, there is a dearth of in-depth research exploring the microscopic mechanisms of this process. Therefore, our research focused on the fructose-1,6-diphosphate (FDP), a typical phosphoryl compound, to gain a deeper understanding of how ultrasound influences the oiling-out process. The focused beam reflectance measurement (FBRM) technology was used to investigate the oiling-out phenomenon of FDPNa3 across various solvent ratios. In addition, the influence of ultrasound on the induction time was studied and the nucleation energy barrier was calculated. Finally, to further unravel the microscopic mechanisms, we utilized molecular simulation techniques to analyze the impact of ultrasound power on the dissolution-precipitation process. Our observations revealed a consistent oiling-out process that attainted a stable state regardless of the solvent employed. Notably, the results of the oiling-out induction time experiments indicated that ultrasound significantly reduced helped lower the nucleation energy barrier of FDP3- ions, thereby dismantling FDP3-clusters in solution. Thus, in turn, shortened the reduced induction time and promoted crystallization. Furthermore, ultrasound reduced the interactions between FDP3-ions and water molecules as well as FDP3- ions themselves. As simulated field intensity increased, these interaction forces gradually diminished, the thickness of the hydration layer surrounding the FDP3- clusters facilitating the disruption of clusters, ultimately enhancing the crystallization process.
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Affiliation(s)
- Pengpeng Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Qian Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Haodong Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Shuyang Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wensu Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Huamei Zhong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Keke Zhang
- Biology+ Joint Research Center, School of Chemical Engineering and Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Fengxia Zou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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Rovers E, Schapira M. Benchmarking Methods for PROTAC Ternary Complex Structure Prediction. J Chem Inf Model 2024. [PMID: 39087481 DOI: 10.1021/acs.jcim.4c00426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional compounds that recruit an E3 ligase to a target protein to induce ubiquitination and degradation of the target. Rational optimization of PROTAC requires a structural model of the ternary complex. In the absence of an experimental structure, computational tools have emerged that attempt to predict PROTAC ternary complexes. Here, we systematically benchmark three commonly used tools: PRosettaC, MOE, and ICM. We find that these PROTAC-focused methods produce an array of ternary complex structures, including some that are observed experimentally, but also many that significantly deviate from the crystal structure. Molecular dynamics simulations show that PROTAC complexes may exist in a multiplicity of configurational states and question the use of experimentally observed structures as a reference for accurate predictions. The pioneering computational tools benchmarked here highlight the promises and challenges in the field and may be more valuable when guided by clear structural and biophysical data. The benchmarking data set that we provide may also be valuable for evaluating other and future computational tools for ternary complex modeling.
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Affiliation(s)
- Evianne Rovers
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
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Roy A, Paul I, Paul T, Hazarika K, Dihidar A, Ray S. An in-silico receptor-pharmacophore based multistep molecular docking and simulation study to evaluate the inhibitory potentials against NS1 of DENV-2. J Biomol Struct Dyn 2024; 42:6136-6164. [PMID: 37517062 DOI: 10.1080/07391102.2023.2239925] [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: 04/01/2023] [Accepted: 06/25/2023] [Indexed: 08/01/2023]
Abstract
DENV-2 strain is the most fatal and infectious of the five dengue virus serotypes. The non-structural protein NS1 encoded by its genome is the most significant protein required for viral pathogenesis and replication inside the host body. Thus, targeting the NS1 protein and designing an inhibitor to limit its stability and secretion is a propitious attempt in our fight against dengue. Four novel inhibitors are designed to target the conserved cysteine residues (C55, C313, C316, and C329) and glycosylation sites (N130 and N207) of the NS1 protein in an attempt to halt the spread of the dengue infection in the host body altogether. Numerous computer-aided drug designing techniques including molecular docking, molecular dynamics simulation, virtual screening, principal component analysis, and dynamic cross-correlation matrix were employed to determine the structural and functional activity of the NS1-inhibitor complexes. From our analysis, it was evident that the extent of structural and atomic level fluctuations of the ligand-bound protein exhibited a declining trend in contrast to unbound protein which was prominently noticeable through the RMSD, RMSF, Rg, and SASA graphs. The ADMET analysis of the four ligands revealed a promising pharmacokinetics and pharmacodynamic profile, along with good bioavailability and toxicity properties. The proposed drugs when bound to the targeted cavities resulted in stable conformations in comparison to their unbound state, implying they have good affinity promising effective drug action. Thus, they can be tested in vitro and used as potential anti-dengue drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Ishani Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Tanwi Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | | | - Aritrika Dihidar
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
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37
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Lohachova KO, Kyrychenko A, Kalugin ON. Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2. Biophys Chem 2024; 311:107258. [PMID: 38776839 DOI: 10.1016/j.bpc.2024.107258] [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: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The main cysteine protease (Mpro) of coronavirus SARS-CoV-2 has become a promising target for computational development in anti-COVID-19 treatments. Here, we benchmarked the performance of six biomolecular molecular dynamics (MD) force fields (OPLS-AA, CHARMM27, CHARMM36, AMBER03, AMBER14SB and GROMOS G54A7) and three water models (TIP3P, TIP4P and SPC) for reproducing the native fold and the enzymatic activity of Mpro as monomeric and dimeric units. The MD sampling up to 1 μs suggested that the proper choice of the force fields and water models plays an essential role in reproducing the tertiary structure and the inter-residue distance between the catalytic dyad His41-Cys145. We found that while most benchmarked all-atom force fields reproduce well the native fold of Mpro, the CHARMM27/TIP3P and OPLS-AA/TIP4P setups revealed a good performance in reproducing the structure of the catalytic domain. In addition, these FF setups were also well-adopted for MD sampling of Mpro at the physiologic conditions by mimicking the presence of 100 mM NaCl and the elevated temperature of 310 K. Finally, both FFs were also performed well in reproducing the native fold of Mpro in a dimeric form. Therefore, comparing the preservation of the native fold of Mpro and the stability of its catalytic site architecture, our MD benchmarking suggests that the OPLS-AA/TIP4P and CHARMM27/TIP3P MD setups at the physiologic conditions may be well-suited for rapid in silico screening and developing broad-spectrum anti-coronaviral therapeutic agents.
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Affiliation(s)
- Kateryna O Lohachova
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine
| | - Alexander Kyrychenko
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine.
| | - Oleg N Kalugin
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine
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El Yaagoubi OM, Ezzemani W, Oularbi L, Samaki H, Aboudkhil S. In silico identification of 20S proteasome-β5 subunit inhibitors using structure-based virtual screening. J Biomol Struct Dyn 2024; 42:6165-6173. [PMID: 37403265 DOI: 10.1080/07391102.2023.2232041] [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: 10/16/2021] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
Proteasome inhibitors have effective anti-tumor activity in cell culture and can induce apoptosis by interfering with the degradation of cell cycle proteins. 20S Proteasome is acknowledged to be a satisfactory target that has persistent properties against the human immune defense and is obligatory for the degradation of some vital proteins. This study aimed to identify potential inhibitors against 20S proteasome, specifically the β5 subunit, using structure-based virtual screening and molecular docking to reduce the number of ligands that should be eligible for experimental assays. A total of 4961 molecules with anticancer activity were screened from the ASINEX database. The filtered compounds that showed higher docking affinity were then used in more sophisticated molecular docking simulations with AutoDock Vina for validation. Finally, six drug molecules (BDE 28974746, BDE 25657353, BDE 29746159, BDD 27844484, BDE 29746109, and BDE 29746162) exhibited highly significant interactions compared to the positive controls were retained. Among these six molecules, three molecules (BDE 28974746, BDE 25657353, and BDD 27844484) showed high binding affinity and binding energy compared with Carfilzomib and Bortezomib. Molecular simulation and dynamics studies of the top three drug molecules in each case allowed us to draw further conclusions about their stability with the β5 subunit. Computed absorption, distribution, metabolism, excretion and toxicity studies on these derivatives showed encouraging results with very low toxicity, distribution, and absorption. These compounds may serve as potential hits for further biological evaluation in the development of new proteasome inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ouadie Mohamed El Yaagoubi
- Laboratory of Biochemistry, Environment and Agri-Food (URAC 36), Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
| | - Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Département de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Larbi Oularbi
- Laboratory of Materials Membranes and Environment, Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
- Supramolecular Nanomaterials Group (SNG), Mohammed VI Polytechnic University (UM6P), Lot 660, HayMoulayRachid, BenGuerir, Morocco
| | - Hamid Samaki
- National Institute of Social Action (INAS), Tangier, Morocco
| | - Souad Aboudkhil
- Laboratory of Biochemistry, Environment and Agri-Food (URAC 36), Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
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Yu SJ, So YS, Lim C, Cho CH, Lee SG, Yoo SH, Park CS, Lee BH, Min KH, Seo DH. Efficient biotransformation of naringenin to naringenin α-glucoside, a novel α-glucosidase inhibitor, by amylosucrase from Deinococcus wulumuquiensis. Food Chem 2024; 448:139182. [PMID: 38569413 DOI: 10.1016/j.foodchem.2024.139182] [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: 11/06/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Amylosucrase (ASase) efficiently biosynthesizes α-glucoside using flavonoids as acceptor molecules and sucrose as a donor molecule. Here, ASase from Deinococcus wulumuqiensis (DwAS) biosynthesized more naringenin α-glucoside (NαG) with sucrose and naringenin as donor and acceptor molecules, respectively, than other ASases from Deinococcus sp. The biotransformation rate of DwAS to NαG was 21.3% compared to 7.1-16.2% for other ASases. Docking simulations showed that the active site of DwAS was more accessible to naringenin than those of others. The 217th valine in DwAS corresponded to the 221st isoleucine in Deinococcus geothermalis AS (DgAS), and the isoleucine possibly prevented naringenin from accessing the active site. The DwAS-V217I mutant had a significantly lower biosynthetic rate of NαG than DwAS. The kcat/Km value of DwAS with naringenin as the donor was significantly higher than that of DgAS and DwAS-V217I. In addition, NαG inhibited human intestinal α-glucosidase more efficiently than naringenin.
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Affiliation(s)
- Su-Jeong Yu
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Yun-Sang So
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Changjin Lim
- School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Chi Heung Cho
- Division of Functional Food Research Group, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Sang-Gil Lee
- Department of Food Science and Nutrition, Pukyong National University, Busan 48513, Republic of Korea
| | - Sang-Ho Yoo
- Department of Food Science & Biotechnology and Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea
| | - Cheon-Seok Park
- Department of Food Science and Biotechnology, Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Byung-Hoo Lee
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam 13120, Republic of Korea
| | - Kyung Hyun Min
- School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Dong-Ho Seo
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea; Department of Food Science & Biotechnology and Carbohydrate Bioproduct Research Center, Sejong University, Seoul 05006, Republic of Korea; Department of Food Science and Biotechnology, Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea.
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40
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Ding Y, Xie D, Xu C, Hu W, Kong B, Jia S, Cao L. Fisetin disrupts mitochondrial homeostasis via superoxide dismutase 2 acetylation in pancreatic adenocarcinoma. Phytother Res 2024. [PMID: 39091056 DOI: 10.1002/ptr.8296] [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: 06/21/2023] [Revised: 01/06/2024] [Accepted: 02/11/2024] [Indexed: 08/04/2024]
Abstract
Pancreatic adenocarcinoma (PDAC) is one of the most lethal malignant tumors with an urgent need for precision medicine strategies. The present study seeks to assess the antitumor effects of fisetin, and characterize its impact on PDAC. Multi-omic approaches include proteomic, transcriptomic, and metabolomic analyses. Further validation includes the assessment of mitochondria-derived reactive oxygen species (mtROS), mitochondrial membrane potential, as well as ATP generation. Molecular docking, immunoprecipitation, and proximity ligation assay were used to detect the interactions among fiseitn, superoxide dismutase 2 (SOD2), and sirtuin 2 (SIRT2). We showed that fisetin disrupted mitochondrial homeostasis and induced SOD2 acetylation in PDAC. Further, we produced site mutants to determine that fisetin-induced mtROS were dependent on SOD2 acetylation. Fisetin inhibited SIRT2 expression, thus blocking SOD2 deacetylation. SIRT2 overexpression could impede fisetin-induced SOD2 acetylation. Additionally, untargeted metabolomic analysis revealed an acceleration of folate metabolism with fisetin. Collectively, our findings suggest that fisetin disrupts mitochondrial homeostasis, eliciting an important cancer-suppressive role; thus, fisetin may serve as a promising therapeutic for PDAC.
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Affiliation(s)
- Yimin Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dafei Xie
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengjie Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenyi Hu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Binyue Kong
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Yamchi A, Rahimi M, Akbari R, Ghobadi C, Aryapour H. Effects of Bacillus in Pectobacterium quorum quenching: A survey of two different acyl-homoserine lactonases. Folia Microbiol (Praha) 2024; 69:913-926. [PMID: 38305961 DOI: 10.1007/s12223-024-01139-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Numerous functions in pathogenic Pectobacterium are regulated by quorum sensing (QS). Two different aiiA genes isolated from Bacillus sp. A24(aiiAA24) and Bacillus sp. DMS133(aiiADMS133) were used. Both genes encode acyl-homoserine lactonase (AiiA), which disrupts QS in Pectobacterium. To investigate the effect of different AiiAs on the inhibition of Pectobacterium carotovorum pathogenicity, two aiiA genes from different Bacillus strains were cloned and the resulting plasmids pME6863 (aiiAA24) and pME7080 (aiiADMS133) were transformed into P. carotovorum EMPCC cells. The effects of different lactonases on virulence features such as enzymatic activity, twitching and swimming motilities, and production of pellicle and biofilm formation were investigated. In EMPCC/pME6863, twitching and swimming motilities, and pellicle production were significantly reduced compared with EMPCC/pME7080. Quantitative real-time PCR (qRT-PCR) was used to measure virulence gene expression in transformed cells compared with expression levels in wild-type EMPCC. The expression of peh and hrpL genes was greatly reduced in EMPCC/pME6863 compared with EMPCC/pME7080. The sequence alignment and molecular dynamic modeling of two different AiiAA24 and AiiADMS133 proteins suggested that the replacement of proline 210 from AiiAA24 to serine in AiiADMS133 caused the reduction of enzyme activity in AiiADMS133.
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Affiliation(s)
- Ahad Yamchi
- Department of Plant Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Maryam Rahimi
- Department of Horticulture, University of Zabol, Zabol, Iran
| | - Ramin Akbari
- Department of Agricultural Biotechnology, Isfahan University of Technology, Isfahan, Iran
| | - Cyrus Ghobadi
- Department of Horticulture Sciences, Isfahan University of Technology, Isfahan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
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42
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Singh AP, Ahmad S, Raza K, Gautam HK. Computational screening and MM/GBSA-based MD simulation studies reveal the high binding potential of FDA-approved drugs against Cutibacterium acnes sialidase. J Biomol Struct Dyn 2024; 42:6245-6255. [PMID: 37545341 DOI: 10.1080/07391102.2023.2242950] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Cutibacterium acnes is an opportunistic pathogen linked with acne vulgaris, affecting 80-90% of teenagers globally. On the leukocyte (WBCs) cell surface, the cell wall anchored sialidase in C. acnes virulence factor, catalysing the sialoconjugates into sialic acids and nutrients for C. acnes resulting in human skin inflammation. The clinical use of antibiotics for acne treatments has severe adverse effects, including microbial dysbiosis and resistance. Therefore, identifying inhibitors for primary virulence factors (Sialidase) was done using molecular docking of 1030 FDA-approved drugs. Initially, based on binding energies (ΔG), Naloxone (ZINC000000389747), Fenoldopam (ZINC000022116608), Labetalol (ZINC000000403010) and Thalitone (ZINC000000057255) were identified that showed high binding energies as -10.2, -10.1, -9.9 and -9.8 kcal/mol, respectively. In 2D analysis, these drugs also showed considerable structural conformer of hydrogen and hydrophobic interactions. Further, a 100 ns MD simulation study found the lowest deviation and fluctuations with various intermolecular interactions to stabilise the complexes. Out of 4, the Naloxone molecule showed robust, steady, and stable RMSD 0.23 ± 0.18 nm. Further, MMGBSA analysis supports MD results and found strong binding energy (ΔG) -29.71 ± 4.97 kcal/mol. In Comparative studies with Neu5Ac2en (native substrate) revealed naloxone has a higher affinity for sialidase. The PCA analysis showed that Naloxone and Thalitone were actively located on the active site, and other compounds were flickered. Our extensive computational and statistical report demonstrates that these FDA drugs can be validated as potential sialidase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akash Pratap Singh
- Infectious Disease Laboratory, Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad, India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Hemant K Gautam
- Infectious Disease Laboratory, Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad, India
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43
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Yan H, He B, He L, Ye H. Screening study on significant Chinese herb for anti-idiopathic pulmonary fibrosis by combining clinical experience prescriptions and molecular dynamics simulation technologies. J Biomol Struct Dyn 2024; 42:6393-6409. [PMID: 37963492 DOI: 10.1080/07391102.2023.2263792] [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: 03/09/2023] [Accepted: 07/01/2023] [Indexed: 11/16/2023]
Abstract
Various techniques such as data mining, network pharmacology, molecular docking and molecular dynamics simulation were used in this study to screen and validate effective herbal medicines for the treatment of idiopathic pulmonary fibrosis (IPF) and to reveal their mechanisms of action at the molecular level. The use of this approach will provide new tools and ideas for future drug screening, especially for the application of herbal medicines in the treatment of complex diseases. Among them, the five identified core targets, including IL6, TP53, AKT1, VEGFA, and TNF, as well as a series of major active compounds, will be important references for future anti-IPF drug development. This information will accelerate the discovery and development of relevant drugs. Meanwhile, this study further confirmed the potential value of four Chinese herbal medicines, including Gancao, Danshen, Huangqin, and Sanqi, in the treatment of IPF. This will promote more clinical trials and practices to confirm and optimise the application of these herbs. Finally, this study is an important theoretical guide to enhance the advantages of Chinese herbal medicines in the prevention and treatment of major and difficult diseases, as well as to understand and utilise the potential efficacy of Chinese herbal medicines. This will further promote the scientific research and clinical application of herbal medicines and provide more possibilities for future disease treatmentCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Haiting Yan
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Beibei He
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li He
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hua Ye
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Li N, Li C, Zheng A, Liu W, Shi Y, Jiang M, Xiao Y, Qiu Z, Qiu Y, Jia A. Ultra-high-performance liquid chromatography-mass spectrometry combined with molecular docking and molecular dynamics simulation reveals the source of bitterness in the traditional Chinese medicine formula Runchang-Tongbian. Biomed Chromatogr 2024; 38:e5929. [PMID: 38881323 DOI: 10.1002/bmc.5929] [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: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 06/18/2024]
Abstract
The Runchang-Tongbian (RCTB) formula is a traditional Chinese medicine (TCM) formula consisting of four herbs, namely Cannabis Fructus (Huomaren), Rehmanniae Radix (Dihuang), Atractylodis Macrocephalae Rhizoma (Baizhu), and Aurantii Fructus (Zhiqiao). It is widely used clinically because of its beneficial effect on constipation. However, its strong bitter taste leads to poor patient compliance. The bitter components of TCM compounds are complex and numerous, and inhibiting the bitter taste of TCM has become a major clinical challenge. Here, we use ultra-high-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) and high-resolution mass spectrometry to identify 59 chemical components in the TCM compound RCTB formula. Next, four bitter taste receptors, TAS2R39, TAS2R14, TAS2R7, and TAS2R5, which are tightly bound to the compounds in RCTB, were screened as molecular docking receptors using the BitterX database. The top-three-scoring receptor-small-molecule complexes for each of the four receptors were selected for molecular dynamics simulation. Finally, seven bitter components were identified, namely six flavonoids (rhoifolin, naringin, poncirin, diosmin, didymin, and narirutin) and one phenylpropanoid (purpureaside C). Thus, we proposed a new method for identifying the bitter components in TCM compounds, which provides a theoretical reference for bitter taste inhibition in TCM compounds.
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Affiliation(s)
- Na Li
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Chunyu Li
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Aizhu Zheng
- The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Weipeng Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yuwen Shi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Mengcheng Jiang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yusheng Xiao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Zhidong Qiu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ye Qiu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ailing Jia
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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45
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Kinnun JJ, Carrillo JMY, Collier CP, Smith MD, Katsaras J. Amantadine interactions with phase separated lipid membranes. Chem Phys Lipids 2024; 262:105397. [PMID: 38740276 DOI: 10.1016/j.chemphyslip.2024.105397] [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: 01/15/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Amantadine, a small amphilphic organic compound that consists of an adamantane backbone and an amino group, was first recognized as an antiviral in 1963 and received approval for prophylaxis against the type A influenza virus in 1976. Since then, it has also been used to treat Parkinson's disease-related dyskinesia and is being considered as a treatment for corona viruses. Since amantadine usually targets membrane-bound proteins, its interactions with the membrane are also thought to be important. Biological membranes are now widely understood to be laterally heterogeneous and certain proteins are known to preferentially co-localize within specific lipid domains. Does amantadine, therefore, preferentially localize in certain lipid composition domains? To address this question, we studied amantadine's interactions with phase separating membranes composed of cholesterol, DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine), POPC (1-palmitoyl-2-oleoyl-glycero-3-phosphocholine), and DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), as well as single-phase DPhPC (1,2-diphytanoyl-sn-glycero-3-phos-phocholine) membranes. From Langmuir trough and differential scanning calorimetry (DSC) measurements, we determined, respectively, that amantadine preferentially binds to disordered lipids, such as POPC, and lowers the phase transition temperature of POPC/DSPC/cholesterol mixtures, implying that amantadine increases membrane disorder. Further, using droplet interface bilayers (DIBs), we observed that amantadine disrupts DPhPC membranes, consistent with its disordering properties. Finally, we carried out molecular dynamics (MD) simulations on POPC/DSPC/cholesterol membranes with varying amounts of amantadine. Consistent with experiment, MD simulations showed that amantadine prefers to associate with disordered POPC-rich domains, domain boundaries, and lipid glycerol backbones. Since different proteins co-localize with different lipid domains, our results have possible implications as to which classes of proteins may be better targets for amantadine.
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Affiliation(s)
- Jacob J Kinnun
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States.
| | - Jan Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Micholas Dean Smith
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37831, United States
| | - John Katsaras
- Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Shull-Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, United States.
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Wang W, Zhong Z, Peng S, Fu J, Chen M, Lang T, Yue X, Fu Y, He J, Jin Y, Huang Y, Wu C, Huang Z, Pan X. "All-in-one" metal polyphenol network nanocapsules integrated microneedle patches for lipophagy fueled ferroptosis-mediated multimodal therapy. J Control Release 2024; 373:599-616. [PMID: 39074587 DOI: 10.1016/j.jconrel.2024.07.063] [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: 04/25/2024] [Revised: 07/07/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
Ferroptosis-mediated multimodal therapy has emerged as a promising strategy for tumor elimination, with lipid peroxide (LPO) playing a pivotal role. However, the therapeutic efficiency is limited due to insufficient intracellular levels of free fatty acids (FFA), which severely hinder the production of LPO. To address this limitation, we proposed a lipophagy strategy aimed at degrading lipid droplets (LDs) to release FFA, serving as the essential "fuel" for LPO production. In this study, the lipophagy inducer epigallocatechin gallate (EGCG) was self-assembled with reactive oxygen species (ROS)-producer phenethyl isothiocyanate (PEITC) mediated by Fe2+ to form EFP nanocapsules, which were further integrated into microneedle patches to form a "all-in-one" EFP@MNs. The metal-polyphenol network structure of EFP endow it with photothermal therapy capacity. Upon insertion into tumors, the released EFP nanocapsules were demonstrated to induce lipophagy through metabolic disturbance, thereby promoting LPO production and facilitating ferroptosis. When combined with photothermal therapy, this approach significantly remolded the tumor immune microenvironment by driving tumor-associated macrophages toward M1 phenotype and enhancing dendritic cell maturation. Encouragingly, in conjunction with αPD-L1 treatment, the proposed EFP@MNs exhibited remarkable efficacy in tumor ablation. Our study presents a versatile framework for utilizing microneedle patches to power ferroptosis-mediated multimodal therapy.
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Affiliation(s)
- Wenhao Wang
- School of Pharmaceutical Science, Sun Yat-Sen University, Guangzhou 510006, China.
| | - Ziqiao Zhong
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China.
| | - Siyuan Peng
- School of Pharmaceutical Science, Sun Yat-Sen University, Guangzhou 510006, China.
| | - Jintao Fu
- School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China.
| | - Minglong Chen
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | | | - Xiao Yue
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China
| | - Yanping Fu
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China.
| | - Jingyu He
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China.
| | - Yuzhen Jin
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China
| | - Ying Huang
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China
| | - Chuanbin Wu
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China
| | - Zhengwei Huang
- College of Pharmacy, Jinan University, Guangzhou 511443, China; State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, Guangzhou 511443, China.
| | - Xin Pan
- School of Pharmaceutical Science, Sun Yat-Sen University, Guangzhou 510006, China.
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Gholampour-Faroji N, Hemmat J, Haddad-Mashadrizeh A, Asoodeh A. Characterization, structural, and evolutionary analysis of an extremophilic GH5 endoglucanase from Bacillus sp. G131: Insights from ancestral sequence reconstruction. Int J Biol Macromol 2024:134311. [PMID: 39094869 DOI: 10.1016/j.ijbiomac.2024.134311] [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: 02/04/2024] [Revised: 07/16/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
Nature has developed extremozymes that catalyze complex reaction processes in extreme environmental conditions. Accordingly, a combined approach consisting of extremozyme screening, ancestral sequence resurrection (ASR), and molecular dynamic simulation was utilized to construct a developed endoglucanase. The primary experimental and in-silico data led to the prediction of a hypothetical sequence of endoglucanase (EG5-G131) using Bacillus sp. G131 confirmed by amplification and sequencing. EG5-G131 exhibited noticeable stability in a broad-pH range, several detergents, organic solvents, and temperatures up to 80 °C. The molecular weight, Vmax, and Km of the purified endoglucanase were estimated to be 36 kDa, 4.32 μmol/min, and 23.62 mg/ml, respectively. The calculated thermodynamic parameters for EG5-G131 confirmed its intrinsic thermostability. Computational analysis revealed Glu142 and Glu230 as active-site residues of the enzyme. Furthermore, the enzyme remained bound to cellotetraose at 298 K, 333 K, 343 K, and 353 K for 300 ns, consistent with our experimental data. ASR of EG5-G131 led to the introduction of ancestral ANC204 and ANC205, which show similar thermodynamic characteristics with the last Firmicute common ancestor. Finally, truncating loops from the N-terminal of two sequences created two variants with desirable thermal stability, suggesting the evolutionary deciphering of the functional domain of the GH5 family in Bacillus sp. G131.
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Affiliation(s)
- Nazanin Gholampour-Faroji
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Jafar Hemmat
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran.
| | - Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Ahmad Asoodeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran; Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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48
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Luo J, Xu L, Yang Y, Huang S, Zhou Y, Shao Y, Wang T, Tian J, Guo S, Zhao J, Zhao X, Cheng T, Shao Y, Zhang J. Stable zinc anode solid electrolyte interphase via inner Helmholtz plane engineering. Nat Commun 2024; 15:6471. [PMID: 39085235 PMCID: PMC11291733 DOI: 10.1038/s41467-024-50890-0] [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: 01/09/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
The inner Helmholtz plane and thus derived solid-electrolyte interphase (SEI) are crucial interfacial structure to determine the electrochemical stability of Zn-ion battery (ZIB). In this work, we demonstrate that introducing β-cyclodextrins (CD) as anion-receptors into Zn(OTf)2 aqueous electrolyte could significantly optimize the Zn anode SEI structure for achieving stable ZIB. Specifically, β-CD with macrocyclic structure holds appropriate cavity size and charge distribution to encase OTf- anions at the Zn metal surface to form β-CD@OTf- dominated inner Helmholtz structure. Meanwhile, the electrochemically triggered β-CD@OTf- decomposition could in situ convert to the organic-inorganic hybrid SEI (ZnF2/ZnCO3/ZnS‒(C-O-C/*CF/*CF3)), which could efficiently hinder the Zn dendrite growth with maintain the proper SEI mechanical strength stability to guarantee the long-term stability. The thus-derived Zn | |Zn pouch cell (21 cm2 size) with β-CD-containing electrolyte exhibits a cumulative capacity of 6450 mAh-2 cm-2 at conditions of 10 mAh cm-2 high areal capacity. This work gives insights for reaching stable ZIB via electrolyte additive triggered SEI structure regulation.
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Affiliation(s)
- Jinrong Luo
- School of Materials Science and Engineering, Peking University, 100871, Beijing, P. R. China
- College of Energy, Soochow Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, 215006, P. R. China
| | - Liang Xu
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, P. R. China
| | - Yinan Yang
- School of Materials Science and Engineering, Peking University, 100871, Beijing, P. R. China
| | - Song Huang
- School of Materials Science and Engineering, Peking University, 100871, Beijing, P. R. China
| | - Yijing Zhou
- College of Energy, Soochow Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, 215006, P. R. China
| | - Yanyan Shao
- College of Energy, Soochow Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, 215006, P. R. China
| | - Tianheng Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Jiaming Tian
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210093, P. R. China
| | - Shaohua Guo
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210093, P. R. China
| | - Jianqing Zhao
- College of Energy, Soochow Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, 215006, P. R. China
| | - Xiaoxu Zhao
- School of Materials Science and Engineering, Peking University, 100871, Beijing, P. R. China
| | - Tao Cheng
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, P. R. China.
| | - Yuanlong Shao
- School of Materials Science and Engineering, Peking University, 100871, Beijing, P. R. China.
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, P. R. China.
| | - Jin Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, P. R. China
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49
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Alharbi AS, Altwaim SA, El-Daly MM, Hassan AM, Al-Zahrani IA, Bajrai LH, Alsaady IM, Dwivedi VD, Azhar EI. Marine fungal diversity unlocks potent antivirals against monkeypox through methyltransferase inhibition revealed by molecular dynamics and free energy landscape. BMC Chem 2024; 18:141. [PMID: 39080756 PMCID: PMC11290312 DOI: 10.1186/s13065-024-01251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
The escalating threat posed by the Monkeypox virus (MPXV) to global health necessitates the urgent discovery of effective antiviral agents, as there are currently no specific drugs available for its treatment, and existing inhibitors are hindered by toxicity and poor pharmacokinetic profiles. This study aimed to identify potent MPXV inhibitors by screening a diverse library of small molecule compounds derived from marine fungi, focusing on the viral protein VP39, a key methyltransferase involved in viral replication. An extensive virtual screening process identified four promising compounds-CMNPD15724, CMNPD28811, CMNPD30883, and CMNPD18569-alongside a control molecule. Rigorous evaluations, including re-docking, molecular dynamics (MD) simulations, and hydrogen bond analysis, were conducted to assess their inhibitory potential against MPXV VP39. CMNPD15724 and CMNPD30883, in particular, demonstrated a superior binding affinity and stable interactions within the target protein's active site throughout the MD simulations, suggesting a capacity to overcome the limitations associated with sinefungin. The stability of these VP39-compound complexes, corroborated by MD simulations, provided crucial insights into the dynamic behavior of these interactions. Furthermore, Principal Component Analysis (PCA) based free energy landscape assessments offered a detailed understanding of the dynamic conformational changes and energetic profiles underlying these compounds' functional disruption of VP39. These findings establish CMNPD15724, CMNPD28811, CMNPD30883, and CMNPD18569 as promising MPXV inhibitors and highlight marine fungi as a valuable source of novel antiviral agents. These compounds represent potential candidates for further experimental validation, advancing the development of safer and more effective therapeutic options to combat this emerging viral infection.
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Affiliation(s)
- Azzah S Alharbi
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia.
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, 21362, Jeddah, Saudi Arabia.
| | - Sarah A Altwaim
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Mai M El-Daly
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Ibrahim A Al-Zahrani
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Leena H Bajrai
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Isra M Alsaady
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai, 605102, India.
- Bioinformatics Research Division, Quanta Calculus, Greater Noida, 201310, India.
| | - Esam I Azhar
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
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50
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Zhu Z, Feng YD, Zou YL, Xiao YH, Wu JJ, Yang YR, Jiang XX, Wang L, Xu W. Integrating serum pharmacochemistry, network pharmacology and untargeted metabolomics strategies to reveal the material basis and mechanism of action of Feining keli in the treatment of chronic bronchitis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 335:118643. [PMID: 39089660 DOI: 10.1016/j.jep.2024.118643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/15/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Feining keli (FNKL) is herbal preparation mainly made from Senecio cannabifolius Less., In recent years, more and more studies have found that FNKL has excellent therapeutic effects on chronic bronchitis (CB). Nevertheless, its pharmacodynamic material basis and mechanism of action are still unknown. AIM OF THE STUDY This study aimed to explore the pharmacodynamic material basis and mechanism of action of FNKL in treating CB. MATERIALS AND METHODS The CB rat model was induced using nasal drops of lipopolysaccharide (LPS) in combination with smoking. Various assessments including behavioral and body mass examination, lung index measurement, enzyme linked immunosorbent assay (ELISA), as well as histological analyses using hematoxylin and eosin (H&E) and Masson staining were conducted to validate the reliability of the CB model. The serum components of FNKL in CB rats were identified using ultra-high-performance liquid chromatography Orbitrap Exploris mass spectrometer (UHPLC-OE-MS). Network pharmacology was used to predict the network of action of the active ingredients in FNKL based on these serum components. Signaling pathways were enriched and analyzed, and molecular docking was conducted for key targets. Molecular dynamics simulations were performed using GROMACS software. The mechanism was confirmed through a series of experiments including western blot (WB), immunofluorescence (IF), and reverse transcription (RT)-PCR. Additionally, untargeted metabolomics was employed to identify biomarkers and relevant metabolic pathways associated with the treatment of CB with FNKL. RESULTS In CB rats, FNKL improved body mass, lung index, and pathological damage of lung tissues. It also decreased interleukin (IL)-6, tumor necrosis factor-alpha (TNF-α), malonaldehyde (MDA) levels, and percentage of lung collagen fiber area. Furthermore, FNKL increased IL-10 and superoxide dismutase (SOD) levels, which helped alleviate bronchial inflammation in the lungs. A total of 70 FNKL chemical components were identified in CB rat serum. Through network pharmacology analysis, 5 targets, such as PI3K, AKT, NF-κB, HIF-1α, and MYD88, were identified as key targets of FNKL in the treatment of CB. Additionally, the key signaling pathways identified were PI3K/AKT pathway、NF-κB/MyD88 pathway、HIF-1α pathway. WB, IF, and RT-PCR experiments were conducted to confirm the findings. Molecular docking studies demonstrated successful docking of 16 potential active components with 5 key targets. Additionally, molecular dynamics simulations indicated the stability of quercetin-3-galactoside and HIF-1α. Metabolomics analysis revealed that FNKL primarily regulated pathways related to alpha-linolenic acid metabolism, primary bile acid biosynthesis, bile secretion, arachidonic acid metabolism, neuroactive ligand-receptor interaction, and folate biosynthesis. Furthermore, the expression levels of traumatic acid, traumatin, alpha linolenic acid, cholic acid, 2-arachidonoylglycerol, deoxycholic acid, 7,8-dihydroneopterin, and other metabolites were found to be regulated. CONCLUSION FNKL exhibits positive therapeutic effects on CB, with quercetin-3-galactoside identified as a key active component. The mechanism of FNKL's therapeutic action on CB involves reducing inflammatory response, oxidative stress, and regulating metabolism, and its molecular mechanism was better elucidated in a holistic manner. This study serves as a reference for understanding the pharmacodynamic material basis and mechanism of action of FNKL in treating CB, and provides avenues for exploring the effects of compounded herbal medicines on CB.
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Affiliation(s)
- Zhu Zhu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Ya-Dong Feng
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Yun-Lu Zou
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Ying-Hao Xiao
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Jia-Jun Wu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Yong-Run Yang
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Xiao-Xue Jiang
- Jilin Yimintang Pharmaceutical Co., Ltd, Siping, 136000, China
| | - Lin Wang
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China.
| | - Wei Xu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China.
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