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Alqarni AM, Niwasabutra K, Sahlan M, Fearnley H, Fearnley J, Ferro VA, Watson DG. Propolis Exerts an Anti-Inflammatory Effect on PMA-Differentiated THP-1 Cells via Inhibition of Purine Nucleoside Phosphorylase. Metabolites 2019; 9:metabo9040075. [PMID: 30995826 PMCID: PMC6523283 DOI: 10.3390/metabo9040075] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 12/13/2022] Open
Abstract
Previous research has shown that propolis has immunomodulatory activity. Propolis extracts from different geographic origins were assessed for their anti-inflammatory activities by investigating their ability to alter the production of tumour necrosis factor-α (TNF-α) and the cytokines interleukin-1β (IL-1β), IL-6 and IL-10 in THP-1-derived macrophage cells co-stimulated with lipopolysaccharide (LPS). All the propolis extracts suppressed the TNF-α and IL-6 LPS-stimulated levels. Similar suppression effects were detected for IL-1β, but the release of this cytokine was synergised by propolis samples from Ghana and Indonesia when compared with LPS. Overall, the Cameroonian propolis extract (P-C) was the most active and this was evaluated for its effects on the metabolic profile of unstimulated macrophages or macrophages activated by LPS. The levels of 81 polar metabolites were identified by liquid chromatography (LC) coupled with mass spectrometry (MS) on a ZIC-pHILIC column. LPS altered the energy, amino acid and nucleotide metabolism in THP-1 cells, and interpretation of the metabolic pathways showed that P-C reversed some of the effects of LPS. Overall, the results showed that propolis extracts exert an anti-inflammatory effect by inhibition of pro-inflammatory cytokines and by metabolic reprogramming of LPS activity in macrophage cells, suggesting an immunomodulatory effect.
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Affiliation(s)
- Abdulmalik M Alqarni
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK.
- Department of Pharmaceutical Chemistry, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University (University of Dammam), Dammam 31441, Saudi Arabia.
| | - Kanidta Niwasabutra
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK.
| | - Muhamad Sahlan
- Faculty of Engineering, Universitas Indonesia Campus UI, Depok 16424, Indonesia.
| | - Hugo Fearnley
- Apiceutical Research Centre, 6 Hunter Street, Whitby, North Yorkshire YO21 3DA, UK.
| | - James Fearnley
- Apiceutical Research Centre, 6 Hunter Street, Whitby, North Yorkshire YO21 3DA, UK.
| | - Valerie A Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK.
| | - David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK.
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Krivov SV. Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate. J Chem Theory Comput 2018; 14:3418-3427. [PMID: 29791148 DOI: 10.1021/acs.jctc.8b00101] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent advances in simulation and experiment have led to dramatic increases in the quantity and complexity of produced data, which makes the development of automated analysis tools very important. A powerful approach to analyze dynamics contained in such data sets is to describe/approximate it by diffusion on a free energy landscape - free energy as a function of reaction coordinates (RC). For the description to be quantitatively accurate, RCs should be chosen in an optimal way. Recent theoretical results show that such an optimal RC exists; however, determining it for practical systems is a very difficult unsolved problem. Here we describe a solution to this problem. We describe an adaptive nonparametric approach to accurately determine the optimal RC (the committor) for an equilibrium trajectory of a realistic system. In contrast to alternative approaches, which require a functional form with many parameters to approximate an RC and thus extensive expertise with the system, the suggested approach is nonparametric and can approximate any RC with high accuracy without system specific information. To avoid overfitting for a realistically sampled system, the approach performs RC optimization in an adaptive manner by focusing optimization on less optimized spatiotemporal regions of the RC. The power of the approach is illustrated on a long equilibrium atomistic folding simulation of HP35 protein. We have determined the optimal folding RC - the committor, which was confirmed by passing a stringent committor validation test. It allowed us to determine a first quantitatively accurate protein folding free energy landscape. We have confirmed the recent theoretical results that diffusion on such a free energy profile can be used to compute exactly the equilibrium flux, the mean first passage times, and the mean transition path times between any two points on the profile. We have shown that the mean squared displacement along the optimal RC grows linear with time as for simple diffusion. The free energy profile allowed us to obtain a direct rigorous estimate of the pre-exponential factor for the folding dynamics.
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Affiliation(s)
- Sergei V Krivov
- Astbury Center for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
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Klein M, Krivov SV, Ferrer AJ, Luo L, Samuel AD, Karplus M. Exploratory search during directed navigation in C. elegans and Drosophila larva. eLife 2017; 6. [PMID: 29083306 PMCID: PMC5662291 DOI: 10.7554/elife.30503] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/11/2017] [Indexed: 11/23/2022] Open
Abstract
Many organisms—from bacteria to nematodes to insect larvae—navigate their environments by biasing random movements. In these organisms, navigation in isotropic environments can be characterized as an essentially diffusive and undirected process. In stimulus gradients, movement decisions are biased to drive directed navigation toward favorable environments. How does directed navigation in a gradient modulate random exploration either parallel or orthogonal to the gradient? Here, we introduce methods originally used for analyzing protein folding trajectories to study the trajectories of the nematode Caenorhabditis elegans and the Drosophila larva in isotropic environments, as well as in thermal and chemical gradients. We find that the statistics of random exploration in any direction are little affected by directed movement along a stimulus gradient. A key constraint on the behavioral strategies of these organisms appears to be the preservation of their capacity to continuously explore their environments in all directions even while moving toward favorable conditions.
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Affiliation(s)
- Mason Klein
- Department of Physics, University of Miami, Coral Gables, United States
| | - Sergei V Krivov
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Anggie J Ferrer
- Department of Physics, University of Miami, Coral Gables, United States
| | - Linjiao Luo
- Key Laboratory of Modern Acoustics, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
| | - Aravinthan Dt Samuel
- Center for Brain Science, Department of Physics, Harvard University, Cambridge, United States
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
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Dai D, Gao Y, Chen J, Huang Y, Zhang Z, Xu F. Time-resolved metabolomics analysis of individual differences during the early stage of lipopolysaccharide-treated rats. Sci Rep 2016; 6:34136. [PMID: 27695004 PMCID: PMC5046119 DOI: 10.1038/srep34136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/07/2016] [Indexed: 01/22/2023] Open
Abstract
Lipopolysaccharide (LPS) can lead to uncontrollable cytokine production and eventually cause fatal sepsis syndrome. Individual toxicity difference of LPS has been widely reported. In our study we observed that two thirds of the rats (24/36) died at a given dose of LPS, while the rest (12/36) survived. Tracking the dynamic metabolic change in survival and non-survival rats in the early stage may reveal new system information to understand the inter-individual variation in response to LPS. As the time-resolved datasets are very complex and no single method can elucidate the problem clearly and comprehensively, the static and dynamic metabolomics methods were employed in combination as cross-validation. Intriguingly, some common results have been observed. Lipids were the main different metabolites between survival and non-survival rats in pre-dose serum and in the early stage of infection with LPS. The LPS treatment led to S-adenosly-methionine and total cysteine individual difference in early stage, and subsequent significant perturbations in energy metabolism and oxidative stress. Furthermore, cytokine profiles were analyzed to identify potential biological associations between cytokines and specific metabolites. Our collective findings may provide some heuristic guidance for elucidating the underlying mechanism of individual difference in LPS-mediated disease.
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Affiliation(s)
- Die Dai
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Yiqiao Gao
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Jiaqing Chen
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Yin Huang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
| | - Zunjian Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China.,State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing 210009, China.,Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China.,State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China
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Banushkina PV, Krivov SV. Optimal reaction coordinates. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1276] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Polina V. Banushkina
- Astbury Center for Structural Molecular Biology; Faculty of Biological Sciences, University of Leeds; Leeds UK
| | - Sergei V. Krivov
- Astbury Center for Structural Molecular Biology; Faculty of Biological Sciences, University of Leeds; Leeds UK
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Abstract
The free energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. The profile together with the optimal coordinate allows one to directly determine such basic properties of folding dynamics as the configurations of the minima and transition states, the heights of the barriers, the value of the pre-exponential factor and its relation to the transition path times. In the present study, we review the framework, in particular, the approach to determine such an optimal coordinate, and its application to the analysis of simulated protein folding dynamics.
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Banushkina PV, Krivov SV. Nonparametric variational optimization of reaction coordinates. J Chem Phys 2015; 143:184108. [DOI: 10.1063/1.4935180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Polina V. Banushkina
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sergei V. Krivov
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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Banushkina PV, Krivov SV. Fep1d: A script for the analysis of reaction coordinates. J Comput Chem 2015; 36:878-82. [DOI: 10.1002/jcc.23868] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Polina V. Banushkina
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences; University of Leeds; Leeds LS2 9JT United Kingdom
| | - Sergei V. Krivov
- Astbury Center for Structural Molecular Biology, Faculty of Biological Sciences; University of Leeds; Leeds LS2 9JT United Kingdom
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